I am no expert, but to me it sounds like the second sentence is more geared towards the future, and the first sentence could be used anytime. For example, I want to take a trip to see my parents at the end of the month, will you be okay with that? Or Is that okay with you?... both work...
However for something happening right now I don't think that I would use will you be okay with that, for example my husband is watching tv and I want to change the channel, I wouldnt say will you be okay with that... it seems too formal or just out of place... I would say Is that okay with you.