I've just put together a small program that will read the ROM list from your cart and show you where each ROM resides in terms of SRAM 'Slots'
That should make it easier to identify where to load/save .Sav files.
It will be added to the Software Download Pack soon.
Please keep the suggestions coming!
EDIT- Has been added.
Using this program, you will get the SRAM Slot number the ROM of interest resides in. Using this number, In the Flash Writer program, you can select this SRAM Slot and Load/Save .SAV files.
As for the example earlier where a particular save was to be shared between multiple LSDJ versions, You have a couple of options. You can either use the above program to write directly to the LSDJ version of interest, or when compiling you can compile 2 LSDJ versions into the 1 SRAM slot (Add the second LSDJ without the SRAM box ticked - this will slot it directly after the first LSDJ version) and both LSDJ versions will share the 1 Save file.
I expect future Compiler releases to be more graphical, with SRAM regions displayed on screen and simply drag the ROM(s) where you would like them placed. Something similar with the Flash software, A graphical representation of the carts contents, both ROM and SRAM icons to drag to a desktop folder, or to the cart.
Edit - New SRAM Manager
A more user friendly SRAM GUI I've been working on. I hope to have it integrated into the main release soon. Simply select the ROM, and press Send or Get. Easy!