The Stage 1 box with what you have will be fine, if the K&N isn't upsetting your car now. Stage 1 is designed to give maximum safe power for casual use on the street. It can be turned off if desired for smog testing etc. You can run the highflow cat and resonator with Stage 1 if you desire, as well as an aftermarket Cat back exhaust, such as the Borla or Greddy.
Optional at this point is the programming cable and program. It can be used with all stages. It allows you to update the map used in the box, as well as tune as you drive (using a laptop). Update maps will be available on our ftp server.
To go to Stage 2 (probably a map), you add the highflow (high temp) cat and resonator (resonator so you keep your hearing). Stage 2 is really intended for racing as it takes you to the edge. You should be familiar with tuning using a wideband O2 unit if you want to run Stage 2 maps. I guess I'm saying it's not for those unfamiliar with tuning an engine. That's one reason it's not for casual driving on the street. Some will use it anyway.
Stage 3 is the incab display/controller. It can be added to either Stage 1 or 2. It allows you to select from up to 3 maps (per ram module - they are removeable/replaceable), and you can display certain engine parameters on the display and change the map entries using just the display and remote controller.
No apology necessary. There are no dumb questions, just dumb answers.