Well, it's a long road.
This is what worked for me:
1. Open Monkeydragon's Boot tool and click on every boot's preview image you want to change. As you click each boot, you'll be asked to select the new png. Once you've changed the boots you want, select IMPORT.
2. You CAN'T ASSIGN a boot to a player with Monkeydragon's Boot tool. You can only check what boot number is being used by that player. In order to do that, you have to use Rinaldo's DBmaster, open fifa.db, go to the "players" tab, and seach for the "shoetypecode" column, right before the accessories columns. (be careful, there are other columns such as shoecolorid or something like that, just ignore them). Remember to save the file of course.
3. Now there's one little extra thing that happened at least to me (so, could happen to you): After assigning boots to fifa.db, I wasn't seeing the assigned boots on the players, neither in the game or checking the players/boot list on Monkeydragon's Boot tool. So I was like "WTF MAN!". But someone told me on Keegan's thread how to solve this: you must delete "D.my squads", located in "My Documents/Fifa 09/D. My Squads". Of course, always making a backup first. Once you've done that, enter the game and save changes to teams, in order to let the game generate a fresh new "d.my squads" file. This way you'll have all boots assignments in the game. BUT I WARN YOU AGAIN: DO NOT TRY THIS STEP UNTIL YOU'RE SURE IT DOESN'T WORK, AND IF YOU DO, BACKUP YOUR "D.My Squads" FILE, OK?
Good luck man