Yeah, some games allow you to save to the RAM cart from in game, but others only use the internal memory of the system. There are also plenty that just create a save file no matter what upon starting up which can be a bit of a pain.
My S-10 battery is dead, and what I did before was a rather tedious process:
1) Start console, and make sure you have the backup cart already inserted
2) Enter RAM menu
2) Format internal memory
3) Play game and save to internal memory
4) When done playing, hit Reset (Not power cycle) to get back to start screen
5) Enter RAM menu
6) Copy file from onboard memory to cart
7) Shut off
From then on when you start playing, just copy the save file you want off the cart and into the memory when you want to play. It's a pain, but it works. Eventually I got S1 with new battery, and that holds my LA saves just fine. I believe the N1/10 PACs have a super capacitor like the duo in them instead of a battery.
I also second the JP carts, they're super duper cheap.