Can Time Machine restore from one large hard drive to two smaller ones?
No. But you may clean HDD to make users and system&amp;library info take no more than 40-45GB (System/Library/Apps) and then use migration assistant ticking only things you need. Or Time Machine if you exclude or move some folders beforehand.

P.S. I wonder if your MBP is pre-unibody one because it is the only type that will benefit from HDD in the bracket in the place of optical disk. For newer MBPs it's better to put SSD in bracket.