No, I never do, beyond letting it do its automated rinse cycle. Here's how I would do it:
1. Start with one 1.75 and one 5 gallon keg. Must be clean, but sanitization not absolutely necessary since you're going to be boiling in them (I typically do anyway, before I store them)
2. Brew the first Pak into the 5 gallon, set it aside and allow the machine to complete its rinse.
3. Brew the second Pak into the 1.75 gallon, and allow the machine to complete its rinse
4. Connect the racking tube between the two kegs' out posts
5. Run the rack cycle from the 1.75 into the 5. You now have ~2.5 gallons in the 5 gallon keg. Ferment as normal.
6. Clean (and sanitize, if you desire) the 1.75G keg
I think you could probably get 3 Paks into one 5G. Folks who know more than I do can chime in on if that leaves enough headspace for fermenting 3.75G of beer, but I suspect it would. In that case, I would redo steps 3-5, after just a quick rinse of the 1.75 keg--no need to clean or sanitize, since you're boiling the same beer in it.
After all that, I'd use the 1.75 to do a deep clean on the machine, and then sanitize it and put it away for next time.