It sounds like you need to take the quilt off the frame and remount it with the unquilted bottom half at the top now. As long as you've gotten to the middle you should be ok. If not, you may need the assistance of someone with a machine with a larger throat.
To quilt a quilt which is too large to get to the middle, you'd have to do something creative like quilt the center one-third of the quilt first, with only the center one-third of the batting in there, take it off and attach each other one-third of the batting one at a time to quilt the top and bottom one-thirds of the quilt. Hope this makes sense. It doesn't sound easy, but it should work.
A thin batting would allow you to get farther in the quilt than a thick batting, of course.