YES YOU CAN
Yesterday I started doing something similar: I have a SCLite and DSTT.
Probably now you're asking how I did it, I installed YSMenu to load them and using GBA Tool Advance to patch some games that don't work right out of the box.
Some recommendations:
1. See if your game has Intro and remove it first.*
2. If you're going to play any Pokémon game do a Clock Fix.
3. Apply SRAM if possible.
4. Optionally trim it.
5. Avoid other patches.
When you load game from YSMenu it will need to format SRAM, say yes and don't worry it's safe to do it.
YSMenu will create a .sav file, play and save.
In order to write SRAM into .sav file you need to turn off and on your DS,
YSMenu will do it automatically but it must be default firmware.
Compatibility seems to be the same only cons are:
I can't find a way to load previous .sav files.
SC Software won't help you saving time with patching process.
I haven't tried GBA Union but i believe it's possible, anyway few games use it.
Tested and working (All games are US version):
Advance Wars
SRAM Patch Required
Castlevania - Aria Of Sorrow
F-Zero - Maximum Velocity
Golden Sun
SRAM Patch Required
Harvest Moon - Friends Of Mineral Town
Kingdom Hearts - Chain Of Memories
Pokémon Advance - Sapphire
Intro+Clock Fix+SRAM Patch Required
Street Fighter - Alpha 3
SRAM Patch Required
The Legend Of Zelda - The Minish Cap
SRAM Patch Required
Let me know if you're able to load .sav files other than those created by YSMenu.
*
Use an emulator or DS because GBA Tool Advance doesn't detect it right, though it will remove it properly