There's definitely some good responses here, but I figure I'll toss a hat into the pile as well. More info for consideration is always good!
While it's true that T3D handles everything as networking, most of that is kinda obscured away from you while scripting, normally. In base terms, if you're writing gameplay, you'll be doing scripts in the server side, if you're doing inputs/gui, you'll be doing scripts on the client side. Then you just have some commandToServer/Clients sprinkled in to bridge between them as needed.
But outside of that, you don't often need to fret on where's what in relation to server/client unless you're getting into some fancier behavior. Doubly so if you're only doing a single player game.
The existing templates do a decent job of getting you set up with a basic framework for gameplay, the networking and some starting content, but the path the scripts take are intermingled and kinda confusing. It's been mentioned, but I've got a draft for a new template based on that t3d-bones one that's more fleshed out and utilizes the modules system. Some changes are coming to it to further refine it for it's integration for 4.0, but if you wanted to have a poke at it, it's here: https://github.com/Areloch/Torque3D/tre ... meTemplate
There's an experimental implementation in T3D already as of 3.9, and as covered in the roadmap, it'll be the primary system for 4.0. I really do like the e/c method because it cuts back on duplication of code and keeps things broken down and managable, as well as letting you build out custom objects without being obligated to jump into the source code.
I'd suggest giving a skim of my work blog, as I do a fair bit of talking about that kind of stff, as well as PBR and other WIP stuff we're doing with the engine for 4.0, here:http://forums.torque3d.org/viewtopic.php?f=8&t=159
If there's anything else you're curious on, or would like some more in-depth breakdowns on, by all means, ask. We've got some rather knowledgable people here, and we're totally keen to answering questions