Biggest difference is when you install an amplifier and then deaden the doors. As for the cables, don't go for fancy ones.. but don't go for generic ones either. Any "branded" cable would suffice (Firland cables are actually a favorite among the budget crowd)

Deadening your doors before installing an amplifier makes little sense because you can't really crank the volume up. And if you don't crank the volume up, door resonance is actually kept at a minimum. If you install the separates and feel something is "off" or nakukulangan ka, get a 4-channel amplifier then deaden afterwards.

As for the deadening, this depends really. Some cars are resonance-happy while some aren't. Take my Sonata for example.. the doors themselves are fully deadened (in, out, and door panel) but I still experience buzzing sounds. If you take a Starex, kahit hindi mo ipadeaden, it won't rattle as much compared to mine. However, general rule of thumb is that deadening your doors is "sulit" because it improves midbass response.

If you're going to upgrade piece-by-piece:
1. Speakers
2. 4-channel amplifier
3. Deadening
4. Head Unit
5. Subwoofer

4 and 5 can be interchanged depending on taste. If you consider yourself to be a basshead, you'd probably go for the subwoofer first before the head unit replacement. But this is fine since I've heard of people using stock FD HUs with the complete set and it doesn't sound bad at all!