Hi and congratulations!
First off, large pebbles are fine, but they have to be larger than the turtle's head so he doesn't eat them. My aquatic box turtle had small river pebbles in her tank and ate them all the time when I wasn't looking. I switched her to slate tiles for a while, but now she has a bare bottom tank and she doesn't seem to mind.
How big is the turtle? The claim that a turtle (or any animal) will never grow larger in a small tank is absolutely false. They stay small if they aren't cared for properly. A turtle should have ten gallons for every inch of shell. So lets say you have a female (though it sounds like you might have a male). They grow up to 12 inches, so that's 120 gallons. Anything less is unfair. I think the petco $1 per gallon sale is over with, so check Craigslist an get that baby into a larger tank as soon as you can!
There is a possibility that it may grow more once you're taking better care of it, but it may never reach full potential (unless it is already full grown). Does it have crazy long front claws, or do they seem reasonable in proportion to its body? Males have super long claws.
Another thing to keep in mind is you're going to need a high quality filter graded for twice the size of the tank you have. Example, if I have a 50 gallon tank, I need a filter rated for 100 gallons or more, because turtles are so messy.
Fill the tank up as high as you can and built an above tank basking area (ATBA) to maximize swimming space.
You can put fish in the tank, but always remember, it will be food eventually. RESs are fast and love fish! Don't put goldfish in the tank because they're too fatty. I've also heard stories of turtles turning on Plecos and taking bites out of them, even if they're smaller than the fish.
Turtles are amazing, and like beardies, take a lot of work and money to care for properly. But once they're established, they're a relatively cheap pet to maintain and actually can have a lot of personality.
Head over to turtleforum.com to learn more about how to properly care for your new pet. The community is much like it is around here, it's a treasure trove of information.