It is the harp size -- distance between needle and pillar (?) of machine -- that determines the amount of quilting space you have available to you. A large quilt eats up quite a bit of that distance as it is rolled up. I think the Juki is a mid-arm machine. The problem you mention is one reason why quilters often prefer long-arm machines.
I don't have a home frame system yet, but I have been reading up on them on the homequiltingsystems group at
http://groups.yahoo.com . I know some of the quilters there have the same setup, so perhaps they can give you some pointers on how to use the space you have.