Ok first thing's first. Thanks so much everyone for all your good comments :D
I know about the bug where you press on pkmn or bag and it doesnt work. this is because of switches, I just haven't got around to doing those parts yet.. EXP works, leveling up works, HP works, and the PC storage thing works!
Ok Firstly, you should probably know something about switches and variables if you are gonna use this in your game.
To use the PC, you will have to get into a battle.. got it? then when nothing is happening (when it is your turn), press F9 and go into the variables part. just scroll right because otherwise you would have to go through lots of variables. anyway go to a variable called ITEMUSE i think... then make it's value 1.
after you have done this press escape a few times to go back to the battle. This will have activated the pokeball item. then after you catch a few, you can go to the PC and withdraw/deposit them, once your party is full and you catch another latios, it should be sent to your PC through a system of variables.. then no more should be sent after your PC is full. ok i am done, thats how you use the PC
Who was it that said the run away option didn't work??? It works! **** well infact. I made it pause for a few seconds then determine to runaway or not.