In my humble opinion, your question is like asking the difference between two, red apples. There will be subtle differences, but clear distinctions are not well defined in my experience. Dreisbach rifles are relatively rare and a Sr., is even more rare, but that does not mean that you don't have a Sr. Pictures (and examination/comparison to other signed rifles) will help immensely. I encourage you to share with the virtual library.
Carving, alone, is not indicative of Sr. The flintlock and percussion distinction could be important, if you are dealing with an original percussion gun. I would predict, with a reasonable degree of certainty, that an original percussion rifle would be a Jr. As I discussed above, Dreisbachs are not particularly common. Those of us who have had on our hands on numerous Dreisbachs tend to find little distinction between the "J*D" signatures. A Sr. should almost always have a sideplate with two turned up horns (much as an early Baum will). Barrel length, barrel type, rifling (or absence), sideplate design, carving style, number and arrangement of inlays, patchbox, butt thickness, trigger style, etc. would all be factored into making a distinction between your rifles, if they weren't both made by the same "John."
An equal mystery with these makers is the fact that the Dreisbach family moved to Ohio around the 1840s. I can look up exact dates, but John, presumably, made rifles in Ohio, along with his cousin (if I have the familial relatonship correct), Samuel. Samuel changed his name to Dresbach once in Circeville, Pickaway County, Ohio, and that gives us a very clear distinction. That same distinction is not present with John Jr. and I think it is difficult to determine a Mifflinburg, Union County, Pennsylvania John Jr. with an Ohio John, Jr., if we are convinced that Jr. continued work in Ohio. Nevertheless, it sounds like you have a great find and I would like to take a look at them.
