I have a few dozen test suites built in Selenium IDE to assist with testing my Store Locator Plus WordPress plugin. Sometimes I need to run a single Selenium test suite. However when I release a new version of the base plugin I want to run a dozen test suites one-after-another.
While not a perfect fit for your use case of creating several "master suites", I did find a pair of Selenium IDE plugins that allow me to create a single "favorites list of suites" and run all of my favorites back-to-back.
It may be possible to investigate & modify the plugin JavaScript to create several different "favorites lists" that may suit your needs. In the meantime you can get at least one "master list of suites" by combining these Selenium IDE add-ons:
After installing each of these add-ons (technically Mozilla Firefox plugins) you will see a favorites button inside the Selenium IDE interface. Mark your favorite suites and you will have your "list". You can now select "Favorites / Run All" from the Selenium IDE menu.
You may want to be careful about the sequence in which you mark your favorites. I marked them in the order I wanted them to run. Open test suite #1, favorite, test suite #2 favorite etc. then "run all". Worked great and shows me the total run count and fail count across all suites (and thus tests) that were executed. The log, sadly, appears to be reset at each suite however.