OK secondary fermentation and bottle conditioning are two different things
Secondary fermentation is not really fermentation but rather the time we give the yeast to clean up some of the by products of the primary fermentation. So when the yeast are really active they make some compounds by accident that can be converted into alcohol later. These compounds are in very small amounts but do affect taste and we would much rather had the alcohol so we leave the yeast in the beer to clean them up. This can be done in the primary (the new way of thinking, less chance of infection and oxidization) or in a dedicated secondary fermenter (and older concept of homebrewing and now most just use a dedicated secondary for bulk aging of certain types of homebrew, others do it as they say it makes the beer clearer and to get the beer off the yeast cake). If I go into too much detail on either one of these methods it will start a raging argument about the need for secondaries or not, suffice to say read up about it and make your own mind up.
Bottle conditioning is probably what your instructions are talking about, this is getting the CO2 to carbonate your beer. So your beer is finished fermenting which you confirm by having the same reading of your hydrometer for two or three days running. Just because the krausen has gone or the airlock is not bubbling does not mean that fermentation is or is not taking place. So after it is done fermenting you leave it for a week or so at the same temp or maybe a few degrees higher to clean up your beer (secondary fermentation) you then bottle your beer. This is mixing a small amount of sugar (dextrose, DME, Honey, brown sugar etc) with the beer to start it fermenting again. This then produces CO2 and because the beer is now in a bottle that CO2 can't escape and carbonates your beer the way it has been done since time began. If you are lucky enough to have a keg then you can skip this and force carb it with a bottle of pressurized CO2. When adding sugar use a bottle priming calculator so you add the right amount normal around 4oz for 5gallons. As too much will lead to bottle bombs and too little will lead to flat beer. Also check out batch priming vs adding sugar to the bottle as it adding sugar to the bottle it is hard to get it just right.
Clem