Factory Bose System is 300 Watts, does this limit me going larger with Sub and Amp?

If you want balanced then you can't really go any higher/bigger with the sub(s) until you up the power to the rest of the system. Unfortunately Blose systems use cheap paper drivers that wont except much more than what they run to them from the factory. 

2 D4 subs, or S2’s will get you to 1 ohm. Look at the Dayton HO series subs, or Audiofrog G series. Maybe take a look at Morel Maximo passive comps for front stage. All great sounding gear that won’t wreck your wallet. If you, or a friend can build a box, you’ll save some cash as well. Doesn’t sound like you can do raw drivers to save cash, unless you go with the Dayton 408 DSP, and go active. If you plan on swinging that in the near future, hold off on front stage until you are active. Then you can save quite a bit by using raw drivers.

D4- Dual 4 ohm voicecoils

S2- Single 2 ohm Voice coil

Raw Drivers- Would be separate midbass and tweeter. generally cheaper but would require you to run a dsp or rustle up some crossovers.

Passive is using the included crossover with a component set. Active would be using a digital adjustable crossover. Amps would be an option but ar enot the best. DSP is the best option as it also includes time allign, summing, eq for each channel, etc....

The Bose speakers are crap so its not hard to get an upgrade. the Morel Maximo are great and hard to beat up to the $250-$275 price range. 

There is a lot to consider but don't overthink it. Sub comp set done. Piece of cake. you can grow your system from there if needed. if you got 100 watts going to some front components and 500 watts to the sub stage it will be worlds different than the Bose system. 

The only ratio you should concern yourself with it the frequency response. Not a random front stage to substage power ratio. Besides... subs need way more power than fronts to be in balance anyway. How much power that is varies from app to app.

Get the subs that you want in there with a bass knob. You can level match with the knob when you're feeling all "essque" and turn it up when you want to wang out.

Factory Bose is actually pretty good, but you can do better when you're ready.

The Maximos are only $150 on Crutchfield. I would suggest getting an amp.

IMO, the best subs out there to do anything and everything well, but you gotta pay to play. I’m running 2 of them trunk baffle and they have no issues playing anything from metal to jazz to edm/dubstep/ trance/ house, etc. I’m running 150w/ch to my front stage, and 1850 to the 2 subs at 1 ohm, and my system is very balanced, if I want it to be. If not, panels are flexing a bit.

Your first thoughts should be sound deadening your sorts properly, then your sub stage, then components. You’ll be surprised what sound deadening itself will do for your factory system...

By the way, Audiofrog just came out with a new line of comps. I think they are called the G90S or something, but they are under $300, and most likely will sound better than anything in this price point.

The Audio Frog stuff is legit, but if you are on a budget I would look at something like the Dayton HO good SQ oriented sub with decent output and great price.