Load your .sav file into it and on the right you will see your Party Pokemon. Right Click on one of them and select "Show in controls" and that Pokemon will appear on the left side of the screen where you will be able to change information for it in the five tabs - Main, Met, Stats, Attacks, OT/Misc. When you have finisihed editing the Pokemon you can return it to its place in the Party, by Right Clicking its position and selecting "Set from controls". Using the selector above the party you can select a PC box. Right click on an empty slot in the box and use "Set from controls" to place it there. When you have finished Save the file.
You can create a completely new Pokemon on the left part of the screen and using the "Set from Controls", as above, place it in the Party or a PC Box