Thanks guys can you recommend good passive sub that would need an amp? For the amp I'm not sure what to look for. I just got these 2 speakers from pioneer and possibly looking to replaced the ones in the front too + add a sub so what kind of amp would I need?
Also some headunits have outputs are they any good or would I be better off with amp? I'm not sure if it's worth to replace the stock head unit.
Lastly would I need to replace battery, alternator etc to power 2 pioneer speakers + sub + possibly front speakers as well? (4 speakers + sub)
For amp the RMS power is important, you can get a mono block amp ( just for the sub) or a 2 channel one ( and bridge the 2 channels). 4 channel is fine too but personally I wouldn't spend more than necessary.
Sub: Brand/model hard to say, the market is filled with cheap brands, and I'm not convinced they are actually worse than the bigger names ( JBL/Harman, Alpine, Pioneer, etc...). It's a gamble often if you can't listen to them before buying. Personally I use an el cheapo ''Raveland'' 12'' sub ( sub/driver itself is 20 euros on Conrad electronics, w. ported enclosure its €50) now for 6 or 7 years and it still sounds better imho than people who have thrice as expensive gear.
Same with amps, it's hard to say, they often lie/exaggerate their (RMS) power, to even ignore the rubbish ''peak'' figure some name, I've used various 2nd hand cheapo stuff and new stuff ( Got 2 no name 2 channel amps, a 4 channel Raveland one, a 4 channel Fusion one, and a 2 Channel JBL). It's really trial and error, a matter of simply trying em out/listening to them.
HU wise you'll want a decent branded one prefferably ( Pioneer, Alpine, Kenwood, etc...), though the ''B brands'' like JVC aren't bad either and at your budget more than sufficient imho.
Battery&alternator: Nope, at the lower end certainly not, it might increase the wear on the battery and perhaps alternator, but this is negligible unless you'll be hanging in more than 500W RMS in the car, which is often pointless anyhow (unless you're deaf or like the attention).
I'd keep the regular speakers on the headunit, more than loud enough with a good headunit. I've experimented with this quite a bit, and found that on the 4 channel amps, hooking up the regular speakers on the amp goes at the cost of sub performance, but that's because I use cheaper amps
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It's hard for me to tell what you like, generally the best boost in sound quality is a good HU and a good compo set in the front doors. If you like more bass then a sub is definitely essential ( I personally love shaking mirrors and feeling the bass on some genres of music once in a while). Personally I think many
**** this up, how many people drive around with just bass and no tone or midrange at all.
Rear speakers ( eg. the 6x9) are very dependant on where they're mounted, on some cars they're absolutely worthless for anything but filling the rear a bit, on other cars they can provide the backbone of the bass ( when lacking sub).
I got these two 6/9 speakers (pioneer ts-a6958) for £4 on car-boot sale and I just couldn't resist it. I checked them and the work and sound way better than my car ones when I hooked them into my sony cinema blu ray head unit at home. However, when I connected them to my car's stock head unit they sound unclear and kind of distorted. Any ideas how could I fix this ? 
. I'd personally be tempted to spend more. It's the most important basis for audio. If you have the choice to skimp on the HU or amps further down ( or the speakers), then I'd skimp on that instead of the HU.
