What PJ said.
YES, you can make a pack with protected cells and yes they work fine. Keep in mind unprotected cells are becoming more difficult to obtain so eventually we may all have to go to packs made this way, or a removable solution ;).
If you fully charge both batteries on a charger that balances them prior to making your pack, you will have the best possible results and the longest possible life. We have packs with protected cells that have been in the wild for 3+ years now and still going strong :o.