Good morning! I feel bad that I can't reply individually to all of your well wishes, but they are very much appreciated!!
As a couple of people have said, we've decided to go with the table for two (just my fiance and I) and my dad and his partner, plus my sister, fiance's parents and the best man will be at a table right in front of us. The more we think about this idea, the more we like it. I'm sure we'll be milling about as well, but it will be a nice chance for he and I to have a moment together.
My dad's partner is none the wiser about the original seating plans, as he hadn't told her yet. I apologised to my dad and mentioned the change of plans last night and he seemed much happier with them, as am I. It didn't feel quite right to have her on the top table, especially since they've not known each other for very long, but as lots of you have pointed out, seating her apart would have been very wrong. I feel that this is a nice compromise.
We're all going for a meal next week as well (dad, me, his partner and my fiance) where I'll ask her if she'd like to come with me, fiance and his mother to test out cake. Feeling much less conflicted. Thanks again to everyone 