Here's a list of commonly asked or general questions. Also feel free to ask here.
Check out the guide for more info.

Q:
How do Pokemon breed?
A:
They need nest boxes to lay eggs. Like normal egg laying creatures, you pen a male near females and let them sit on the egg until it hatches. Note that only Pokemon of the same species and stage of evolution will breed, and the egg will be of the stage (This is a DF limitation).

Q:
I cant use <item>.
A:
There's sometimes issues with items being in storage containers (bags / barrels / bins). Either setting the stockpile to feed into the workshop or making a stockpile without storage and dumping the items out of them should make them available for workshops.

Q:
Why do Pokemon only have 1-3 moves?
A:
This is mostly a balance thing, insuring Pokemon aren't too powerful and overly FUN whilst creating a sense of varying strength between different species and stages of Pokemon. Attacks tend to use velocity modifiers to simulate different influences (like power/STAB) so giving them a bit of a limit insures fun and not FUN.

Q:
How do Pokemon evolve?
A:
After entering conflict or by using the evolve reaction, they will gain an (e) next to them. This means they are in the process of evolving and will eventually transform into their next stages. Every month is assumed to be 1 gained level, so they will transform after the same amount of months as their required level.

Q:
What about special requirements for evolving? (Trading/Friendship/Stones/Location)
A:
Using the evolve reaction, trading causes evolution instantly whilst friendship takes 1 month. Those requiring certain locations evolve after being in a specific biome or using the appropriate item, and those that require specific items have the "Evolution Chamber" workshop.

Q:
How do I use the Evolution Chamber / Trimming Table / Pokemon Center?
A:
Designate a pen/pasture on top of the workshop, then put the Pokemon in it. Once they are there, start performing the reaction. It can take a few tries for it to actually work, so it is recommended to do it with many Pokemon at once. When it is applied, the Pokemon should feel "apathetic" (and flash on classic mode). For evolution, any Pokemon that has an (e) next to their name won't be affected, due to evolving previously or going to evolve.
Note: Large gems won't work for evolution.

Q:
How do I catch / recruit Pokemon?
A:
You can select them at the character creation screen in adventure mode if your civ has tamed them, otherwise you can claim tame ones. In fortress mode you do like any other animal, with cage/animal traps. Pokeballs are anti Pokemon ranged weapons, dealing extra damage to them and not much against others.

Q:
How do I play as a Pokemon?
A:
Using the PMD content will allow you to do so, both in fortress and adventure mode. Otherwise adding either [OUTSIDER_CONTROLLABLE] or [LOCAL_POPS_CONTROLLABLE] to the raw of the desired Pokemon is required for adventure mode (without PMD content).

Q:
How can modded races use the stuff from this mod?
A:
Go to the mod files and in the extra folder there's "entity_zpokereactions" and "creature_zpokeitemuser". Replace YOUR_ENTITY_HERE with the modded entity and YOURCREATUREHERE with the associated creature of that entity and move the two files into the objects folder of the installed mod.