I'm not sure what you're asking there, but I always use GBA ExpLoader to manage my 3-in-1. It's quite simple to use, and it handles SRAM patching automatically. If you go that route you should disable the multi-save feature (you just edit the .ini file in a text editor and remove the # from the appropriate line) to avoid confusion.
Another thing you should know is that the EZ4 Client and the 3in1 tool (not to be confused with the 3in1 ExpPack Tool) should not be used on roms that might be played from PSRAM, or lost saves will result. Either use a loader that handles SRAM patching automatically, or patch the games with GBATA instead of the EZ4 Client.