I'll 2nd the question of whether you are planning to tear off the old roof. I'm assuming yes, since you mention that you will replace some plywood. Since your roof is leaking already, I'd recommend a tearoff, but you technically can install a 2nd layer of shingles if you currently only have one layer. If you decide to do a 2nd layer, make sure you use longer nails (maybe 1/2" longer to be safe). Most shingle manufacturers call for the nail to penetrate wood decking by 3/4" or to penetrate all the way through plywood decking.
Do you have a coil nail gun? If not, you can likely rent one (or maybe 2), which would make installation much quicker. Just be sure to properly adjust it so as not to over drive the nail. Also, be sure that you're driving the nail perpendicular to the surface; a nail driven at an angle can more easily tear through the shingle.
Don't skimp on the sealant that you'll use on flashings and exposed nails (you'll probably have at least a couple exposed nails on the ridge). I recommend Sonolastic NP1. Especially try to avoid the clear sealants as they don't seem to last as long, in my experience, as the colored sealants.