Had a situation last week that I hadn't seen addressed on this thread (but I could have missed it), so I wanted to share.
Long story short, I ended up with an anytime/
any park FP due to a ride closure the night before, along with an anytime FP just for DHS for that day due to a ride closure that morning on RnRC. The any park FP was listed first on
MDE with the anytime DHS FP listed second. I wanted to ride Toy Story, but I didn't want my any park FP to be used first. I asked the manager type CM that was at the entrance to Toy Story. He said the system should be smart enough to use my more limited anytime DHS FP first, similar to if I had a timed FP for just Toy Story itself.
He was right. It took off my second listed FP (the anytime DHS) first and I was able to use my any park FP at Epcot later that day.