I'll just go through and answer your questions one at a time....
You can repot before they're through, but by disturbing and possibly breaking roots, you risk the plant dropping its flowers prematurely.Two of the Phals are blooming. I beleive that I should wait until they stop before repotting
Phals. are monopodial, meaning they only have one "foot" or growth stem. Unless the main plant has developed a baby off to the side with its own roots, there's nothing to divide or split up, so this plant would just need repotting.One is very root bound and probablly needs to be split into 2 plants.
We use styrofoam peanuts here to cover the drainage holes of our pots. They're light, which saves on shipping, and they don't decompose. Just make sure you don't use the biodegradable kind made out of starch, or the colored (pink and green) kind which has chemicals in it that can harm the plant. For Phals, straight bark as a medium is ok, but it doesn't have much water retention, which means you'll be watering pretty often to keep the plant healthy. You might want to go with an orchid potting "mix" that has other things in it besides just bark. Most home improvement stores carry it.I have planned to use bark as a medium, however I've heard about using styrofoam shipping peanuts as a base for the bark, is this an acceptable practice?
It's not uncommon for dendrobium canes to yellow, shrivel, and dry up. They will do that in preparation for putting out new canes from the base of the remaining old ones. There's not a whole lot you can do to stop the process. With dendrobiums, strong light is absolutely key. But, if the plant was already going downhill at the store, you might unpot it and check the roots to see if they're rotted. Dends like their roots to dry out a little between waterings so, depending on your growing conditions and watering habits, straight bark for it may be just fine.If [the denrobium] doesn't get better I'm going to repot it and seperate the sick canes out. What medium would be the best to use?
If the large black areas on the leaves are a fungus, the neem should help. If they're a bacterial infection, you might want to pour some listerine on a paper towel and wipe the leaves down top and bottom with that.
If you've never repotted before, you can check out a step by step guide on the basics of it in the CARE section of our site.