I am fighting coccidia myself so I will tell you what I have found out. Don't worry too much about the Coccidia but prepare to be really good at cleaning. I have 7 beardies. 2 came from breeders (one has low coccidia), 2 are older rescues (one had high coccidia) and 3 are from pet store chains (all have coccidia at different levels). That is how common it is depending on where you got your beardie from (age seems to factor in too). In fact, it is so prevalent in beardies that there are some who think that it is a commensal organism. This is why vets usually do not treat coccidia unless the levels are high or the beardie is showing symptoms such as weight loss, lethargy, diarrhea (smelly) etc. Usually dragons can either clear it themselves or they are not affected by low levels. It is during periods of illness or stress that their levels can skyrocket and then it may affect them adversely. This is the reason many folks want to get rid of all coccidia in their dragons to be safe but it is not easy to do. Since you only have one dragon you have a good chance of getting rid of it though.
I could be wrong, but Metronidazole (Flagyl) is not usually prescribed alone for coccidia. Did they perhaps send you home with metronidazole and something called albon or ponazuril?
As for cleaning, recommended things to do are:
1. Take everything out of your tank that you can. Minimal, barebones furnishings is what you are looking for.
2. You can put your beardie on paper towels. As soon as there is a poop remove and replace all the towels. Replace the towels once per day regardless.
3. You can soak your wood in diluted bleach or ammonia solution, rinse well then pop it in the oven at 285 degrees for 1 hour.
4. There is conflicing opinions on the best cleaners to wipe down your tank but ammonia and steam are thought to be the most effective. Quaternary Ammonium cleaners (quats) or diluted bleach sprayed on and left for 15 minutes are also thought to be effective. I believe Wipe out has quats in it. I'm not sure about using hot water since I thinkit has to be 165 degrees to kill coccida.
5. Clean up all poops ASAP, then clean with ammonia/quats/steam. Some folks recommend cleaning the tank each day or setting up a temp tank since cleaning is a pain.
6. Don't put your furnishings back in the tank till the coccidia is gone.
7. I have read that allowing your beardie to drink from their
bath water is a no-no during treatment. This is due to the coccidia coming off the dragons skin, floating in the water then getting ingested when they drink.
You can get a Shark steam cleaner for a reasonable price. Steaming is pretty easy with no chemicals but you have to remove your dragon while you use it and then let it dry/air out before they go back in.
Anitibiotics and parasite treaments are hard on beardies. Get some probiotics (soy yoghurt, Acidophils+, bene-bac etc.) to replace their normal gut flora. Makes sure they stay
hydrated too.
Good reads:
http://www.beardeddragon.org/articles/parasitecare/
http://www.exclusivedragons.com/HealthIssues.html
http://www.beautifuldragons.com/Parasites.html