When you buy a license (or two in your case) and log in in sitefinity.com you can say for what domain you want each license to be valid.
The two sites would run independently from each other. You simply apply the corresponding sitefinity.lic to each project. That should do the trick.
However when you are really talking about the same site in two languages I would recomend and pay the extra 1000 USD for the Standard Edition (SE 2000 vs. 2 SBE each 500 USD)
a) Maintaining would be easier - only one update not two
b) Resources - one SF would surely use less RAM then two SF instances
c) Rights - You only have to add users on one site
d) backups - less space
e) all benefits that come with SE like: more then 50 pages, mulitlingual in more then two langues, forms, analytcis and stuff
I assume that you bought 2 SBE to save 1000 USD. I think in the long term it would not pay off. Maybe try to talk to sales if you can switch and pay the difference.