She'll have them wherever she chooses and unfortunately that might not be where you planned! You just have to make the boxes extra-inviting to her - she has to feel safe there after all. If she wants to be around you a lot, maybe go and sit with her by the box for a while and try and settle her in there, so that she can still see and hear you etc.

If she really doesn't feel like any of the places you're suggesting are right for her, then unfortunately you're just going to have to watch her like a hawk and be ready with a little "mobile birthing box" - I have an incontinence mat (bit like the things that go on nappy changing stations only not plastick-y feeling) which I managed to get under my girl when she decided to have her kittens on my bed - didn't get there before the first sac broke and spilled water everywhere, but I did manage to get it under her before any blood and goo!

Just make sure she doesn't decide the litter tray is the best place to go - if it's a hooded one maybe take the top off it so you can keep an eye on her if she decides to go in there.

Good luck