It looks like all of the problems with running games from PSRAM are caused by the EZ4 Client. If you want to run a game from PSRAM, patch it with GBATA instead. If you're only going to run games from NOR, it shouldn't matter which program you use to patch the games.
If the games have been patched with GBATA, you should be able to run games in both NOR and PSRAM modes without having problems with the saves getting overwritten.
You can run any GBA game (that works on the 3-in-1) from NOR. You can only run games up to 16MB from PSRAM.
Games that use 128KB (AKA 1 Mbit or 1024 Kbit) saves are a bit more complicated. They can be patched with GBATA, and if they still work afterwards, they can be run from PSRAM. If they do not run or save properly after being patched with GBATA they must be patched with the EZ4 Client instead, and then they can only be run from NOR.
GBALdr doesn't do much that the EZ-V kernel doesn't do in terms of running games, but it does have a few other features like the ability to dump GBA roms. If the EZ-V does everything you need/want by itself, feel free to not bother with other software.