AlterEgo, should've just shot me an sms man ;p
let me answer your doubts/questions one by one.
1- ~90% of all current ps3 games work (which means some don't work ;p). CoD2: Modern Warfare 2 is one of the few that don't work. before downloading a game, always take a look here for your game to know if it works or not (
www.psjcl.com )
2- make sure there's one original disc inside the ps3 at all times (before launching a game from BacupManager, this will ensure all the games that are reported to work perfect, they'll work on ur ps3 also).
3- whenever you copy a game to ps3 hdd, make sure there aren't any unnecessary 'wrapper' folders, for example hdd0/.../Gamez/GameName/PS3_GAME.SFB is right, and ur BM should detect the game, but hdd0/.../Gamez/UnnecessaryFolder/GameName/PS3_GAME.SFB is not right, as there's an extra folder in the hierarchy.
4- for now, the best strategy is, avoid ALL game update prompts. no need to isntall any game update, its the most easy way to avoid trouble.
5- if a game is giving black screen, make sure you delete all old savegames of that game, as well as any installed update data of that game, before trying it on BM.
This should solve many of your problems.