Steve, your rootstock is probably EMLA M111, a good semi dwarfing rootstock. Yes, the rootstocks are clones/cuttings that are rooted in special beds. You can actually get away with planting these deeper than you would expect because there's no real root crown to speak of. All of the roots are adventitious so if you plant it deep you just get more adventitious root growth, which, in this case is just fine, AS LONG AS THE GRAFT IS WELL ABOVE SOIL LEVEL. Once the tree gets established in it's final planting spot it will develop a root crown over time, which should be respected as with all trees.
Having cloned/cutting rootstock allows for choosing specific traits such as disease resistance, soil preference, climate preferance, and dwarfing characteristics. Proper varieties of seedling rootstock, however, will produce longer lived and much larger and more majestic apple trees.
With some of the seedling rootstocks (M111 is one of them I think), when planting you want to make sure that none of the roots go upwards. They should all be lateral or downwards in the hole. Upwards facing roots may have a tendencies to put out root suckers under certain conditions.
Steve, from your description it sounds like you are getting lots of sucker growth from below the graft. I'm not sure why that is happening, but I don't think it's because of this particular rootstock.
Today we grafted apples onto the EMLA M7 rootstock (a bit shorter of a tree than is produced by the M111). If I remember correctly the varieties were Canadian Strawberry, Golden Russet, Northern Spy, Amata, and something else. The cherries went onto Mahaleb rootstock and the varieties were Evan's Bali and Masabi, both tart cherries good for pies and fresh eating.