Even if you did get totally clear beer into the bottles (which you should strive for), if you are bottle conditioning there will be a small layer of yeast/trub that develops from the conditioning process (fermentation of the priming sugar you added). The only way to avoid this is to keg carb and then bottle from the keg.
As mentioned though, if you have a hefe, getting some of that layer in the glass is not bad at all. Some commercial beers of the style advise that you swirl that layer up and try to get it in the bottle. Just for future reference, if you have an IPA or something where you want that layer to stay behind in the bottle, you just have to be careful pouring... pour in one smooth motion, let the bottles sit upright in the fridge for at least a few hours before you pour them (longer is better) which will get the sediment mostly cold-crashed out.
Personally I just wouldn't cold crash the fermenter unless you have a way to 100% deny oxygen (air) incursion. On this point, if you have to ask right now, you don't have this ability. (Also most people on their first brew don't really have a way to cold crash a 5 gallon fermenter anyway)
"Whirlpooling" at ~170 for post-flameout hop additions is fine for IPAs; I don't think it applies to hefes though, or at least none of the recipes I recall seeing. So for your beer, for next time, I would:
1) Flameout
2) Chill as quickly as possible for as long as your immersion chiller is working efficiently. Agitating the wort during this time will make the chiller work better. I just stir the wort with the chiller itself. After about 15 minutes you can make a judgement call; lots of people continue with the chiller until the wort is at pitching temp, but, in the interest of not sending so much water down the driveway, I stop with the immersion chiller at about 120F or so; ymmv on this.
3) Let the kettle settle out. Hop material and any other solids will mostly drop to the bottom in about 20 minutes; sometimes I'll wait as long as an hour; just make sure the lid is on the kettle and it is sealed up as much as possible as the wort is subject to getting infected at this point. You can stir it into a whirlpool at the start and all the trub will collect in the middle. Or if you don't bother it will just be in a uniform layer across the bottom. In practice I don't see a big difference between the two.
4) Transfer to sanitized fermenter, leaving most of the trub behind in the kettle. If some trub is transferred, no big deal though.
5) Cool the rest of the way to pitching temp if needed. In my early days this meant putting the fermenter in an ice bath. Note that if you do this, you can get a layered temp in the fermenter pretty easily, so get as much of the wort below the water line as possible.
6) Pitch, ferment... skip the secondary.
7) If you are willing to spring for carbonation drops, you can prime the bottles and fill them straight from the fermenter. This guarantees that each bottle is primed evenly, and also avoids the oxygen exposure of racking to a secondary bottling bucket for batch priming. The drops are going to be a slight cost adder vs. batch priming with a corn sugar solution. If you do go with the solution, make sure it is mixed as evenly as possible without splashing the wort.
8) Leave at room temp for two weeks
9) Pop a couple in the fridge for 24 hours and give them a try.