I would say go for a single 12" sub to start off with because I personally think that that sized sub in a boxed that is matched to the sub would be better as it will cater for all different kinds of music so doesnt matter if you start listening to anything different, coz 10s are really punchy but cant handle long bass notes really & 15s arent very punchy & are very good for long bass notes so a 12" would be perfect I reckon
& as for a choice of subwoofer, I would suggest the directed studio 12", very good sub & an even better price! & upgrade your componants to! 6.5" sized woofer/mid might be a better choice. As for choices, I would say Focal would be definetly the best to go for for front speakers. I personally have the Poly Kevlar 3 Way componant set & they amazing, however alot of work is needed to fit these in any car! (unless you own a porsche!!!) So I would stick to 2 way componants & focal polyglass 165v2s are very good! But It all depends on what your budget is mate! If you give a budget, I can suggest a number of different models of speakers, but if you just want a make, then I would say Focal or some PG.
& make sure you amp up your front componants, because if you choose the right amp, you are looking at a serious improvement in sound quality & overall loudness. As for you 6*9s, Move them away from the parcel shelf if you are putting a sub in your boot, Stick them in your rear quarter panels if you can, otherwise sell them on. I had 6*9s in the rear quarter panels in my last motor, & it actually complements 6*9s, & this is coming from me (who is not a good fan of the speaker!!) They werent overwhelming, but did create that surround sound effect by producing some rear fill, However, it took a bit of work to fit them in there. & of course, I had to create an enclosure for them!
hope that helps mate
Mark