It is very common to graft weeping maple varieties onto a standard to get them up off of the ground and produce a faster tree (it's not really required, as staking the young tree can get the same results, but takes longer). The scion is the desired variety that was grafted on top, and the rootstock is, of course, the part with the roots.
If your rootstock is sending out branches, you will almost certainly want to prune them off, as the rootstock is often more aggressive than the grafted variety. The sooner you do this the better, especially in Japanese maples which don't take kindly to heavy pruning. If you do cut off anything large, be careful that you don't cut into the collar near the trunk, and that you keep the cut clean and dry.
