With one full season under your belt and a conference championship to show for it, you are not doing too bad.
I took a quick look at your team and you appear to have pretty good talent. Not top 10, but certainly competitive. TE, OL, and DL are the areas most lacking.
Now to your question....if you don't have proper talent, nothing else matters....thats why I mentioned talent first.
1. Pick 2 or 3 offensive formations and 2 or 3 defensive formations and focus on them. I only practice 2 O formations and 3 D formations. You can still use the others, but its tough to have proper talent to run both the Shotgun and the Wishbone (for example).
2. On offense....don't try to be too fancy. Set up a "normal", a "losing by a few", a "losing by a bunch", and a winning gameplan. Run those for several games before making any "tweaks". One game will NOT tell you anything. You might also want to have a mostly run or a mostly pass version of your "normal" plan.
3. On defense, decide if you want to focus on stopping the run or stopping the pass as your first priority. Then you can decide what to use as your "base" defense (4-3 and Nickel seem to be most common). If you choose run 4-3 and Nickel for example, you can still run the 5-2 or Dime under certain circumstances, but you probably won't have the proper personnel or the Formation IQ to run either of those extremes well on a consistent basis.
4. On offense, I just run my offense, pretty much without regard to the opponent. I try to mix it up a little, but I don't make any wholesale changes based on a specfic game. On Defense, I do look at tendencies and make a FEW tweaks based on that. However, I've found (over times) that my base defensive setup works well and is a mix of 4-3, 4-4, Nickel and Dime.
There are some formations/coaches that I still have trouble defending against (gantincbus you know who you are!!!)
You have to experiment a great deal and certainly have to recruit the players that fit in your system. Lastly, look at your competition in your conference. It does not do you any good to decide to focus on run stopping with a base 5-2 and some monster DLs if all of your competitors are running the Shotgun full time and throwing it deep to speedy WRs.