There's some general C recommendations that I can provide, but that's a pretty broad question so it's hard to really address it. Are you looking for ideas for how to structure your data, for how to update the graphics, for how to accept user input? Why have you chosen LabWindows/CVI over another C compiler?
In general, I would recommend looking up Design Patterns and finding a pattern that approximates the way you're trying to make your project work. Build around something that people already know is good rather than trying to reinvent the wheel. Are you wanting to cycle through a sequence of events regularly, but have the order change based on the program's input? Use a State Machine. Are you wanting to process some data entirely independently from the rest of your program? Look into parallel loop structures.