I use Biomark PIT tags b/c they're based on open standards. I know that the Trovan tags are encrypted, and thus can only be read by Trovan readers. Technically the encryption can be broken and still read, but this is illegal. It is a stupid trick these manufacturers use to have you locked into their one little niche (if the reader ever messes up, breaks etc, guess who you HAVE to buy another one from???). Biomark tags are not encrypted and can be read by any reader that conforms to the open standards set forth by the ISO standard 11784/11785 guidelines. I've used these on dozens of animals and it works great for me.
As far as how much experience is needed, I'd say have an experienced individual show you how to use them properly, and then you'd be able to mark your own animals (just do it supervised the first few times). I've used them to mark juvie watersnakes with no ill effects. I don't go between the ventrals like some people do, I actually go betwwen the 3/4 or 4/5 dorsal scale rows, work the needle under the ribcage and then inject the tag interperitoneally. If needed, I use some dermabond to seal the wound up if needed (more important on smaller animals).
Personally I'd use a injectable flourescent dye to mark smaller animals (we use them to mark TINY salamanders, and the marked spots glow blue/orange/red or whatever color you injected). Using this sysetm of different colors of dye and different injection locations you can uniquely mark MANY MANY MANY different animals. Then as the animal gets older I'd use a PIT tag.