Are you trying to make composite plants that have transformed roots but un-transformed aerial tissue? I've been using A. rhizogenes to make composite legumes to study what a gene does in the roots. For this, I used pENTR followed by gateway cloning into a binary vector. From there it was very easy to transform into A. rhizogenes and then infect the roots. With pENTR, just be sure to include the 5' addition to the forward primer so that you can do the ligation. For making the composite plants, I'm attaching the protocol that I am using from the Medicago truncatula handbook (http://www.noble.org/medicagohandbook/).