If you have any chance that children or other people not accustomed to darkroom chemistry will visit your darkroom, of course you should label all the chemicals clearly. This is regardless of the origin of the bottles. Brown color can, of course, be an extra precaution, but not enough IMO if you are concerned about safety, and it has its own drawbacks. Clear labeling with big labels works for both "soda bottles" and commercial chemistry bottles, brown or clear.
Squeezing is almost too easy, much easier than with accordion bottles because of these facts:
1) thin neck -> more visual precision in solution level & less air captured there even if you close the cap too early. Not possible with accordion bottles at all!
2) clear plastic -> you can actually see the solution level. Extra benefit: you can evaluate the solution for color and insoluble matter
3) Tight caps that have a clear point when they are tightly closed. I've found most accordion bottle caps worse.
So, you squeeze like this: almost close the cap. Squeeze the both sides of the bottle between your thumb and forefingers, see how the solution is rising in the bottle. Simultaneously, use your other hand to close the cap, to the point when you cannot squeeze anymore. Then open the cap a bit, so that squeezing is possible again but with restricted speed. Then, squeeze until you see the solution hit the cap, or you can feel how you cannot squeeze anymore, as all of the air has come off from the small gap where solution cannot pass. At the same time, without loosening the grip, close the cap. Actually writing or reading this description will take much more time. It will take 5 seconds to do it properly.