Use the GBA Union function. In the Supercard patcher there's an option which lets you make the DS game think that such and such game is in Slot 2.
can you get the R4 to think the same???
Not unless you had one of these three things:
1. The original cart
2. An old style GBA flashcart that had no ROM selection menu (or had that option)
3. Witchcraft
If you had a slot 2, then... off the top of my head, use the slot 2 card and get the save like that (I'm pretty sure most slot 2 cards have the GBA Union or equivalent feature) and then transfer the save to your slot 1. e.g. if you had a SCL and an R4, then you get your Pokemon rom onto your SCL, do the Union, get the Pokemon, then use the R4 save convertor then put that onto your R4. Might be a better way, but this should work.