Root stock is a term used to refer to the material hosting the scion in grafting. Root stock typically has advantages over growing the scion on its own roots - increased vigor or hardiness, dwarfing abilities, disease resistance, etc.

Bare root refers to a method of how plants are harvested and sold for market. Bare root is just that - a tree, shrub (almost always deciduous) or perennial that is dug during dormancy and sold without a soil root ball - the roots are exposed. Generally quite seasonal in availability, bare root plants are easier to transport and plant so are usually less expensive and often larger than containerized selections and because they are most often offered while dormant and should be planted right away, they seldom experience any transplant shock.

I won't go into the details on grafting and propagation - lots of books available to address this and a bit too complicated for this forum. Just continue to read and get as much info as possible. As to whether you should start with cuttings or seedlings, you can best answer that by how long you are willing to wait before you can achieve any harvest. The smaller and less developed the plant, the longer you will have to wait and the more hands-on you are (ie germinating seeds, taking cuttings, preparing grafts, potting up) the more expensive the end result becomes. May just be simpler, cheaper and faster to plant young trees in situ and tend to their care. Once your orchard is established and bearing fruit, you may want to delve into the more technical aspects of propagation.

Best of luck. You may want to consult your county extension office for resources in your area for plants or additional information most suited to your climate conditions.