I'm not sure if this has already been covered, but I have found a way to backup your original CD console save RAM by loading a bios on the Mega SD:
1. Load a BIOS ROM for Mega / Sega CD, preferably the one that matches the CD hardware you are using.
2. Insert a game disc and before it boots, press any button other than start to enter the CD console's built in menu.
3. On model 1 consoles. enter the 'Option' menu, on model 2 / CDX consoles enter the 'Memory' menu.
4. Copy the desired saves from Internal RAM to Cartridge RAM and power off the console.
5. Remove the micro SD from your Mega SD and connect to a PC. Inside the 'BUP' folder, there will be a SRM file with the same name as the BIOS you just loaded. This contains the saves you just copied over.
6. Copy and rename the SRM file to match the name of the ISO you wish to play.
7. Insert micro SD back into Mega SD and play.
Certain games may not support reading from Cartridge RAM, for those games copy the saves from Cartridge RAM to internal RAM using the CD BIOS' built in menu. I have used this method to transfer my original 20+ year old saves for Snatcher and Sonic CD and they work perfectly.