Simple solution:

Save your connections with different names -- even if you're logging into the same system.

1. Click a connection name (don't double-click), and click the "Load" button.

2. Click the "Colours" section of the "Window" tree to the left.

3. Adjust background, foreground, and any other colors by clicking the name, then the "Modify" button, and then clicking the color you want.

4. Important! Click the "Session" section of the tree, where you should still see the session you loaded. Click the "Save" button.

From now on, when you connect using that session, it will have that color scheme. Just do the same for the other sessions to differentiate.