What system do you have now? The base one or the Shaker 500?
I replaced the speakers in my '05 since my stockers had been blown ever since I bought the car (I had the shaker 500 system). The $50 kenwoods I got on amazon sounded a lot better but nothing incredible. They did get rid of the terrible rattle from the blown stock speakers and that's all I really got them for so mission accomplished... I'll replace those with some nice components eventually but that's a ways out... but I digress.
Couple weeks after replacing the speakers I installed my new head unit and that made a night and day difference. It sounds significantly better. I wired the door subs to the subwoofer output on the head unit which lets me control the bass level and, more importantly, the crossover points. That made it so I can send just bass to the 8" woofers rather than the high frequency signals that ford sends to them stock. This means that the stock door subs hit a lot harder and sound a lot cleaner than they ever did with the stock head unit.
At the end of the day I'd definitely recommend replacing the head unit. If you have the Shaker 500 in your car already then I'd probably recommend getting a head unit and some inexpensive speakers first, then adding subs later... but then again bass isn't my priority and it might be for you so that's up to you.
As for adding subwoofers? One vs 2 is really a matter of taste. I personally will eventually be adding a single woofer so I can keep the weight down a bit and conserve the already somewhat limited trunk space. Only reason to add 2 subs is if you want more power than you can get from a single one.
2005 Windveil Blue GT (MT)
93H Bama tune, JLT Series 3 CAI, FRPP CMDPs, Pype bomb super system, 3.73 gears, Steeda shift bushings, Saleen short shift block
Steeda ultralite springs, Tokiko D-specs, J&M Extreme joint UCA/LCAs, PHB, C/C plates, bumpsteer kit, Steeda Q1S wheels, 2011 GT brakes, 275/40R18 Sumi HTR Ziii tires