You'd want to consider these:
1. your chain, and what you have in total current demand
2. the ampere rating for the tranny you are considering.
Polarity considerations are important in so far as you need to be careful not to fry the circuit - it depends from box to box, but some will fry if you feed the wrong polarity to it. Otherwise, you can cut the wire and reverse it if you are cheap (albeit with shrink wrap, good soldering), or buy a proprietary reverse connector.
Rechargeable batteries are a better option in many regards, but get the Nickel Metal Hydride ones and stay away from the Nickel Cadmium ones, which are prone to 'memory effect', i.e. they lose their charge very quickly if you do not observe good practice in discharging.... Batteries, rechargeable or otherwise are particularly good with some distortion circuits which may sonically benefit from a voltage feed of 6 - 7 volts, sometimes 5 volts when the voltage drops with use, i.e. if you want the extra clipping. This of course is variable, and if you are clever you would build a voltage regulator to feed your box consistenly low voltage.
With regard to time & pitch altering efx, you'd sometimes want a higher voltage feed for cleaner headroom. Most chips can take up to 24v, and several time/pitch circuits have high current draw, so a rechargeable battery is not necessarily your best bet. The caveat is that this matters if you are in a recoding environment, in a live environment, several aspects that many musicians seem to worry (true bypass, headroom, etc etc)about don't really matter that much unless your stage sound and venue acoustics are exceedingly controlled and excellent beyond 90% of performance venues.
Speak to Edder. I don't know if he makes custom stuff anymore, but he'd certainly tell you how to get yourself wired .