On the Setup tab of the Project form, you can press the "Add Run-Deck" button and you will get the option to add multiple .bdf and .f06 files. When HyperSizer runs, it will generate multiple .PM1 files (one for each run-deck).
Notes:
1) The FEM grids and elements will only be read from the first run-deck so if you have multiple run-decks, make sure the first one you enter (run-deck 1) contains all of the components that you want to analyze. If your second run-deck has less elements than the first, thats ok, it just means that when HyperSizer analyzes components that are not in your second run-deck, it will assume zero loads for all of the load cases in that run-deck.
2) Make sure your load sets and nastran subcases are unique in each run-deck.
3) You can only have a single thermal case per run-deck.
Let me know if you have more questions.
Phil