Hi Adam,
take a look at BReps -- they are the way to go when combining, uniting, substracting, etc. various parts of your geometry. For boudary conditions you can make use of colors (their names) which can be applied robustly even when topologiacal changes occur in the model during shape variation. You should be able to find everything to get started within the help menu of CAESES.
Cheers,
Heinrich