I have this issue frequently. The key is to make sure before your stays that you have separate stays listed on SPG.com, each with different confirmation numbers. Note those different confirmation numbers, and then check out as you wish--though paying for them separately makes it understandably easier for the hotels to properly allocate the stays. If you have issues after the fact, then providing the separate confirmation numbers helps research more easily correct the situation.

I love being able to get credit for up to 3 rooms for every stay/night. But the mechanisms for SPG to properly credit these are glitchy. Marriott doesn't allow this, but I'm hopeful that Marriott will see the benefit of elite credit for multiple rooms--as opposed to staying elsewhere that will give credit.