General questions

This is just in case me and Kirb accidentally find a pure seed in our travels, but what exactly do they do in the RP?
Also, if you find a joy seed, do you just use it and automatically get a level up? Or what?

Another question; for attacks that work differently in the PMD games than in the main games (eg: destiny bond), which attack's effects do we follow?

I think I need to make a directory of moves and items to explain their effects and stuff really. The moves one would be harder to do hough since everyone uses their moves differently in order to be strategic. Well.... I'll answer your item queries first and then look up about the Destiny Bond thing.

Pure Seeds;
When eaten a Pure Seed will merely warp the pokemon eating it, further on into the dungeon. Not much of a beneficial effect in rp to be quite honest, but there you go. You could always use i for some weird plot based thing, where your characters get separated. But iI'll leave it to you to decide how you use it.

Joy Seeds;
Yes, your level will automatically go up, but you would not just change your level in your character Records pages. A Joy Seed will merely give you the required amount of pages you need to level up. Eg, if you had 24 pages... it would give you that one extra page to get to 25 and your next level.

On the matter of moves with difficulty to carry out in the rp, I suggest just speaking to the person who is getting hit or using the move. If it is an npc doing the move, speak with whoever is controlling said npc. Ripple and I had the same problem with Keyami's Foul Play move. We ended up deciding that whenever Keyami used it, he'd just use a pokemon's own momentum against them to slam them into something. With destiny bond, I suggest making it so that it only activates if the opponent attacks you, as to where they'll take the same damage as yourself instead of fainting if you faint. This way if you happen to be stronger than your opponent, you may survive the attack while still defeating your opponent or vice versa. One way to rp it out is to have threads wrap around your opponents, so when they attack you the threads cause damage by cutting into or sending powerful shocks to the opponent.
Personally, moves will differ from pokemon to pokemon and roleplayer to roleplayer. It essentially is however you learned the move. Akuroma's confusion attack is basically him making the other pokemon have hallucinations, and Keyami's foul play is, again, him using the enemy's momentum against itself, yet confusion is seen as a weak telekinetic force in the games and foul play has no specific way of usage. As such when you do make the directory of moves, only have it as a baseline, don't make it written in stone. of course a ghost type move will never affect a normal type, but a ghost type move doesn't always have to be the same, boring way unless specifically specified.