Richard, I'm no expert but the MapQuest program is really large. I hope you have the 16 GB Mini because if you have the 8 GB Mini you would use most of your storage space on that one program. The map files take up 1.3 GB of memory while the full Map Source program takes 1.6 GB including the maps.
The best solution would be to install the basic program on the mini and store the maps on a SD card, however I'm not sure if you can split it like that.
But to answer your question, yes that is how I have installed several programs to my Mini. On your desk top simply insert the CD and an Flash drive. Don't run the installation but rather copy the contents of the CD to the flash drive. Insert the flash drive in the Mini and click on the D drive. If the installation program doesn't start running open the D drive window and click on the 'setup.exe file and it should start loading.
What I think might also work is to install two flash drives, one blank and one with the copy of the MapSource installation
CD. When it asks you where you want to install the program choose the blank flash drive. The installation will install most of the files on the blank flash drive but will make the changes to the system needed to run the program. This of course would mean that you must plug in the Map Source flash drive when you want to use the program,