First off, no "secondary fermentation" happens in the "secondary vessel.
You shouldn't rack a beer to secondary until fermentation is complete...
"Secondary fermenter" is actually a misnomer and a mistake many brewers make....the secondary has nothing to do with he process of "secondary fermentation" which is part of the normal yeast life cycle, one of the stages of fermentation.Which is done in your bucket or carboy.
The secondary we are referring to is also called a "brite tank" it is the carboy where people move their beer to clear, or to add fruit, or hops for dry hopping... and to let the yeast and other things fall down...
There is a "secondary fermentation stage," but it happens in your primary along with lagtime, and reproductive phase. It is part of the life cycle of the yeast, and it all happens before it is time to move it to a clearing tank, (secondary vessel or brite tank"
Here's John Palmer's explanation of the Secondary fermentation Phase
The fermentation of malt sugars into beer is a complicated biochemical process. It is more than just the conversion of sugar to alcohol, which can be regarded as the primary activity. Total fermentation is better defined as three phases, the Adaptation or Lagtime phase, the Primary or Attenuative phase and a Secondary or Conditioning phase. The yeast do not end Phase 2 before beginning Phase 3, the processes occur in parallel, but the conditioning processes occur more slowly. As the majority of simple sugars are consumed, more and more of the yeast will transition to eating the larger, more complex sugars and early yeast by-products. This is why beer (and wine) improves with age to a degree, as long as they are on the yeast. Beer that has been filtered or pasteurized will not benefit from aging.
The reactions that take place during the conditioning phase are primarily a function of the yeast. The vigorous primary stage is over, the majority of the wort sugars have been converted to alcohol, and a lot of the yeast cells are going dormant - but some are still active.
The Secondary Phase allows for the slow reduction of the remaining fermentables. The yeast have eaten most all of the easily fermentable sugars and now start to turn their attention elsewhere. The yeast start to work on the heavier sugars like maltotriose. Also, the yeast clean up some of the byproducts they produced during the fast-paced primary phase. ...
It's easy to see how confusing the terms are...that's why we try to get outta the habit of saying secondary fermentation...and just say secondary...or bright tank (mostly just secondary, dropping fermenter or fermentation, since fermentation should be finished before you rack it to the secondary. After the hydrometer reading stays the same for 3 days.
New brewers often rack way too early, and often interrupt the secondary phase because of this, and that is why you often see panic threads about Krausens forming in secondary, because the yeast was really still in the primary phase of fermentation when it was moved.
And it starts building a krauzen house again....
If you do choose to use a "bright tank" it's best to wait til fermentation is complete, you know that by taking 2 gravity readings over a 3 day period. If the grav hasn't changed, then you can rack it without having a krausen develop...though sometimes it does anyway.
Many of us nowadays forgo a bright tank and just leave our beers in primary for 3-4 weeks, then bottle...We only use a secondary if we are adding something to the beer, such as fruit, dryhopping or oaking the beer, otherwise we just leave the beer alone and let the yeasts clean up the beer at their own pace. Or if we added fruit, like pumpkin in the boil and want to get the beer off the goop.
If that wasn't clear, Donman sums it up pretty well;
I thought Palmer was actually pretty good about differentiating between Secondary Fermenting and Secondary Fermentation. I found Papazian to be less so. When I read Papazian the first time I was left with the exact impressions that you have and when I look at my brew logs from 1992 I was regularly doing 4 and 5 day primaries and then secondary. He actually made me feel like the sooner off the yeast cake the better.
You are confusing secondary fermentation with secondary fermenter. Very easy to do.
Secondary fermentation occurs while the yeast is still in solution immediately after the conversion of sugars to alcohol. During that time there is tons of proteins and partially digested sugars in solution in addition to the waste products of the yeast, plus any esters and fusel they create while they ferment. During secondary fermentation the yeast will clean up these esters, and the fusels, and reabsorb a lot of their waste products.
Once this process is complete if you choose THEN you can rack to the Secondary Fermenter. This is a also called a bright tank or clearing tank and it is where the sedimentation occurs. This is where the most of the proteins and other detritus fall out of solution and the beer clears. Yes, the yeast is still present in this tank but because the vast majority has been left behind in the primary tank any benefit from the yeast at this stage is greatly diminished.
So if you haven't figured it out, NOTHING should be happening in the Secondary (brite tank) except you beer clearing......
You will find Many of us here leave our beers in primary for a month, it is actually very good for the beer to leave it around that long...it improves taste and clarity vastly...
There are several dozen threads about long primary or no secondary, at least three a day asking your question...if you wanna know what it does and why we choose to do it, just do a thread search on those key words...there's like at least one new thread on it every 2-3 days so there's plenty of info.
This question gets asked and answered several times a week, so the info is here, Even John Palmer in "How To Brew" mentions the benefits of waiting...
Leaving an ale beer in the primary fermentor for a total of 2-3 weeks (instead of just the one week most kits recommend), will provide time for the conditioning reactions and improve the beer. This extra time will also let more sediment settle out before bottling, resulting in a clearer beer and easier pouring. And, three weeks in the primary fermentor is usually not enough time for off-flavors to occur.
But if you do choose to rack, WAIT TIL FERMENTATION IS COMPLETE.
Unless you subscribe to my pal Boerderij_Kabouter's way of thinking...then do it that way, there's many ways to skin this cat, and ultimately either way will make beer.
It is ultimately your call......
Me personnally I leave nearly all my beers in primary for a month and then bottle and only use secondary, if I am lagering in the cold for several months, adding something like hops or fruit or oak to the beer to flavor it, have had a lot of fruit like pumpkin added to the boil that carried over into the fermentor, or if it is a huge beer that I feel benefits for months of bulk aging time.......
If my beer is NOT meeting any of the afore mentioned conditions, which is usually 95% of my beers...then it is long primary and then straight to bottle.
There is already a ton of info on here about this topic. Almost daily, but some of the older threads are more detailed, if you want to get deeper into the reasons why. You will find a lot of people may not answer since they have answered this questions several times already, and see it daily. BUT if you want to see some of the better discussions I suggest that you search for the terms "No Secondary" or "Long primary."
There have been some really in depth discussions on it, with some great info to help you make up your mind...but you will find it is really a matter of personal preference, usually based on anecdotal evidence. Me personally, I have noticed my beer tastes and looks better leaving it in primary for a month.