The premise is that you first download and install the game patches for all your games. Use multiMAN or PS3 Game List or PS3 Game Updater to download the patches that are 3.55 compatible (<3.56).
Once you have your games updated with the latest patch, use the PS3 FTP client to update the APP_VER of your PARAM.SFO to 99.99 (or any number higher than the latest patch version of your game).
When you launch your game, it will compare its APP_VER vs the version TITLEID-ver.xml in the Playstation server. If the APP_VER is lower than the version specified in the XML in the server, the game will ask for update. If the APP_VER is higher, the game will continue loading and will not ask for update (saving you from a potential mistake: update the game with a non compatible patch).
99.99 should be enough for almost all games. However, some games may require specific APP_VER. For these ones, don't change the PARAM.SFO or rename back the PARAM.SFO.bak to PARAM.SFO.
You can update the APP_VER without download & install the patches too.