If they're over wood, you should be able to just dope further and sand them out. For future reference, you can dampen silkspan (or tissue. I suppose) and lay it over the pre-doped wood. I use enough dope and sanding to get a bit of a sheen, before laying the tissue on. I cannot vouch for your particular choice of dope/thinner, but using Brodak clear and thinner has worked well for me. Several coats and some sanding to take out high grain and level the surface, followed by paper, and finally brushed-on thinner to adhear the paper to the original dope has worked well with no wrinkles. The problems I've encountered are two fold, but not visible in final finish:
1) The new "silkspan" has not adhered as well as the old stuff (do a SSW Forum search for lots of commentary).
2) If you don't let the dope really dry for several hours, I'm convinced that the paper can "float" up some, causing a heavier finish.
Otherwise, no wrinkles. You can have as smooth a finish as you want.
So...you should be able to sand and dope for a perfectly level and smooth finish, even though you have wrinkles now.
Edit: Having re-read the post, I should comment that, if there's a wrinkle, then there's excess paper. Often this can be accomodated by working the paper some with the fingers, while doping. However, I often cut slits in the paper and either overlap or cut out more material to minimize any overlap. In either case, sanding removes that excess paper, sometimes even before the work is "dry (as long as it's only detached in tiny areas, like along a narrow wrinkle, and not a large-area 'blister'). If there is bare wood, yes, you can easily patch and sand the edges. If a large area is not attached, remove it and patch, sanding later along the edges. In both cases, tearing the paper edges, rather than cutting them makes feathering easier. It seems nerve-wracking sometimes, but after a few successes, you get to expect things to come out all right. Trust me!
SK