As far as I know, it shouldn't be much of an issue.
Just copy and paste your custom units in object editor from map 1 to map 2, as you would normally do, with or without sharpcraft. You can also export/import your units data by going to File > Export all objects data
As for the custom models files, in the import manager, you may import and export files too (one at a time, or all at once), by going to File > Import/Export.
To my knowledge, Sharpcraft does not interfere with this kind of manipulation, so it should be harmless.