Choose all ... this uses config /opt/retropie/configs/all/retroarch.cfg - you did that already.
The parameter for the save pathes can made dynamical if you use $1
So /home/pi/RetroPie/savegames/$1 for a GameBoy game will be /home/pi/RetroPie/savegames/gb
/home/pi/RetroPie/savegames/$1 for a NES games will be /home/pi/RetroPie/savegames/nes....
In my humple opinion /home/pi/RetroPie/scripts/SavePath.sh "all" "/home/pi/savegames/$1" is the best setup
It saves STATEs and SRM files into one location in depence of the system (gb, nes, snes) and used the config file for all base settings.
Instruction point 5 can be understand following. Usually the setting for savefile_directoryand savestate_directory are commented out with a #.
So you have to set them "active" by uncommenting them.
So if you already have setted them up like savefile_directory = "/home/pi/RetroPie/savefile" you are fine.
So the script will always overwrite this: like savefile_directory = "/home/pi/RetroPie/savegames/gb"
Hope I was clear now ;)
I suppose you are running RetroPie on RaspberryPi. If you do, you should be able to overcome the issue by using symbolic link (command named "ln" with parameter -s). You enter the folder with the savegame in command line via ie: "cd /home/pi/RetroPie/roms/psx" and then you make the symbolic link via ie: "ln -s gt2_(simulation).srm gt2_(arcade).srm" The first one should be the already existing file and the second one should be the name of the link. After that the gt2_(arcade).srm points to the gt2_(simulation).srm and that means whatever disc you load both of them would actually load the same file.
I have experienced the same issue in RetroPie 4.1, 4.2, and 4.3: the the *.srm file gets created when doing an in-game save, but the game can't seem to find the save file when you go to load your saved progress. I have tried various BIOS files, unfortunately without success.
This tool MPKEdit does what you want. load the .N64 file then save it as a normal .MPK which can then be converted to Mupen's .srm format with whatever tool you have.
Edit: OK so you're trying to extract EEPROM saves from an MPK file, not trying to use an actual controller pak save. Open the .N64 in MPKEdit, then Hold Control (save icons for note should turn red) and click the save icon. then rename it as required, convert it to SRM as required, etc.
For anyone wanting to attempt this with Stretch, it's actually a lot easier. The owncloud client and command line client are now included in Stretch. Run apt-get install owncloud-client-cmd to install the client this script needs. Then edit the script so that it is checking for owncloudcmd in /usr/bin/owncloudcmd instead of /usr/local/bin/owncloudcmd. Run the edited script through sudo and away you go. Everything works swimmingly aside from the fact that old saves are not moved to the new location.