If these are truly separate installs, with their own databases, they should not interfere with each other at all.
If you wish to exclude servers from scanning on one installation, you must add the machines' NetBIOS names to the configuration console under Scanning Options\Computer Exclusions. Please note as well that excluded machines are not automatically removed from your database. To remove these machines, select them in the configuration console under Lansweeper\Scanned Computers and hit the Delete button.