As an alternative you could create soft/symbolic links from the roms folder on your two usb drives to the systems roms folder on RetroPie.
The command to do so would be.
ln -s file1 link1
An example of linking psx roms from usb drive to the psx roms folder on RetroPie
ln -s /media/usb/psx /home/pi/RetroPie/roms/psx
This will create a soft symbolic link of all the files in the specific folder.
Look at the file1 as the source and link1 as the destination and change them to the correct location of each folder.
This is what i have done and it works most of the time but sometimes it does not as it looks like the mount of the USB name changes when restarting the RPI and that breaks the soft links. This approach is great if you don't want the usbromservice to move everything and just want to keep only the roms on the USB drive.
Edit: I think that maybe by using both soft symbolic links and then make sure that the USB drive always will be mounted as ex. USB0 or Your USB Drive then it would work great.