While this isn't difficult to do, it is more fiddly than I ideally want. There is, however, a command that can be run in a Command Prompt to set install mode and another one to switch it off.
I always forget what these commands are so figured by posting them here it would both give me easy access to remind myself, but also that I find posting here helps things stick in memory anyway.
So to set XenApp into install mode open a command prompt (Win + R followed by typing cmd) and type the following:
change user /install
Once the program has finished installing, switch the server back to normal by entering the following command:
change user /execute