For best results it would be a good idea to remove any existing paint before applying POR-15. Especially if you have significant rust in the area since there may be the beginning of corrosion below paint that appears stable. If this isn't feasible, just scratch up the existing painted surface before applying POR-15 and don't expect the job to last forever.
If they are accessible I'd recommend doing both sides as well. This goes for any area where you have holes. Sure, this isn't always possible, but if you can totally encapsulate the rust you'll stand a better chance of stopping it.
For those nickle size holes I'd recommend our Epoxy Putty (
http://porshop.com/porshopfilpu.html). Prep the area with Marine Clean and the Metal Ready as you would when applying POR-15 before you put the putty down. Then there's no need to prep the area again before putting down your POR-15. If you sand the epoxy smooth just wipe the area down with a damp rag before coating with POR-15 (water only - never any solvents as they may leave a residue that will inhibit POR-15's ability to grip).
Thanks!