ReefMaster reads and indexes tracks when you "import" them, and saves position and depth information to the workspace database. It does not store the sonar imagery in the workspace file - this would result in huge workspace files. Instead, sonar imagery is read directly from the original sonar file, which is why the sonar files must be present in their original locations when using the sonar viewer or sidescan mosaic.
Ideally you would copy over your sonar files from your SD card and store then somewhere on your hard drive. Not only will this result in better read performance (depending on what kind of card reader you have, and how it is connected to your PC), but it will ensure that files are available in their original import location when you need them (if you rely on an SD card, then the drive letter could change between insertions, for example).