You're right- it isn't possible to use SmartMatches between two tree owned by the same member.
If the two files are similar, it also won't be a good idea to merge- because it will create many duplicates.
So my suggestion is that you create a separate account with a different email address, craete a new site and upload the GEDCOM file to it. This will enable Smart Matching between your two trees. Another option is to just add the extra information from one tree to the other, manually.
Hope this helps- let me know if you have any more questions.