Hi Martin,
With a reference to the TL-VI wired to the VIs that are loaded into the subpanel, you should be able to do what you are trying to do, for instance get a ref to the TL-VIs menu, and manipulate it.
But with just the information about the apps, it's hard to know if the sub-panel approach is recomendable.
Here are some random thoughts about some of the alternatives i see:
Independent apps with launcher This is simple, your apps do not share any GUI functions (not the old fashioned way at least) and have no natural common denominator or shared resources. You could build your apps as source distributions and the launcher could easily launch new apps you add to the suite.
Subpanels I'd use this if the apps have a limited set of behaviours, and more important, they have some common ground. Perhaps all the apps use different sets of hardware but the report is the same.
Kind of Object Oriented approach Regardless if you use subpanels or not, if your apps are somewhat alike, it could be good to try and sort out how they are constructed. Perhaps you could put all the common functionality of the TL-VI into a few VIs that use some kind of repository (perhaps an uninitialised shift register).
Straight Edge OO Using classes and inherritance you get some pretty good ways to handle this kind of a problem, but with legacy code it's more like shoulda-woulda-coulda
Hope you stopped reading before I messed it up completely.
If you didnt, and you are indeed messed up, you have my deepest apologies.
/Marcus