Welcome, and congrats on your new little boy =)
Pin holes are also a sign of high ammonia, which could easily be the case since he just came from a pet store cup.
For now keep an eye on it, do regular water changes since it's still a new tank and you don't want to break up any natural cycle that it is going through with the filter.
In a 5 with filter you will be wanting to do 50% weekly water changes, every so often siphoning out the gravel.
If you wish to use something, Stress Coat works well with regrowth of fins. You can use that as a conditioner, or add in some drops along side your normal conditioner. (Always use full dose of conditioner when you do water changes.)
If you see black edging starting around the hole, or at the edges of his fins and it is flaking/crusty/shredding then you can start the AQ salt treatment.
1 teaspoon AQ salt per gallon, regular water conditioner (and/or stress coat) 100% daily water changes for 10-14 days. Best to put him in a QT container/tupperware/cup to make changes easier (premix the treatment in a gallon jug to make water changes easier when doing less then a gallon QT container) and float/tape the QT in the tank, 76-78*F to keep him from getting too cold.
I would wait on any treatment until you are 100% sure it is rot, because the salt can harm internally if in prolong use, as well as the bacteria/fish can easily become immune to the salt over time and it will highly diminish the beneficial/healing properties of the salt. AQ salt should only be used when you know for certain it is needed.
Also don't just automatically go to the over the counter fish meds.. Quick Cure is actually not a good thing to use, neither is Bettafix, and most other "fixes" as they contain a tree oil that has potential to harm the labyrinth organ in which bettas use to breathe. Conservative is always highly recommended use over meds unless it is very severe. (Conservative = AQ salt & Epsom Salt)
Good luck and let us know how it goes =)
Last edited by Myates; 10-11-2011 at 08:07 PM.