I suggest, if you're going to use a track system with a road bed to use one manufacturer, thus eliminating any problems with connections. Alot of people you'll see use either cork, or that new(er) Woodland Scenics foam for roadbed, and place the track on top them selves.
There's various advantages to both, the foam and cork being a "softer", or "sound deadening layer". The WS foam will allow softer hits on the rail joints which is an obvious benifit for our micro worlds, the cork to a lesser extent and both should elminate "echo" from the joint hits, and the "metal on metal, on top of wood" echo's. These roadbeds also allow for the most varition in track plans, and the track pieces are in a MUCH larger varity. As far as I know there's no flex-track plastic roadbed manufactured.
BUT intern the plastic roadbed provides easy of assembly, and tear down, if need be. To a lesser extent it should deaden the sound. Its also fairly prototypical straight from the box, and would require little or even, maybe no effort to look "ok". And it can ALLWAYS be upgraded with some simple gravel over the plastic for ballast. Once again though, lower number of track parts available. Also the interchanging of various companies is some times impossible, and the plastic trackbeds do not have an NMRA standard to connections, like "normal" track does.
Then it comes to track... Code 100, Code 83, Code 70 (for HO), what do you choose? most beginer sets come with code 100. Code 83 is close to prototypical (although Code 81, which is rare, is closer), and Code 70 replicates a lighter weight rail, for say yards an branchlines. If I were you I'd stick to code 100 for the added reliablity, but Code 83 will surfice if you're more of a detail freak.
Then there's the Nickle silver/ brass debate, just use NS, trust me...
In all its up to you, no one here will look down on you for your choices!!!
P.S. I think this is one of my most detailed replies yet!