As far as the speaker wire is concerned, you don't really need to run new speaker wire; maybe add some extension wire depending on where you want to put the 6x9's. But if an audio shop is handling that then that is their problem. If you buy some don't get the bottom of the barrel because a lot of times they cheap you on the gauge size.
I would have to agree with going with 4x6's for the rear and putting them in the stock location or getting creative. I redneck engineering them into the little cubby holes below the armrest in the back.
What are you asking about the RCA's exactly? 10 Feet is pretty short unless you're not going far with them. I have 10 footers but they go from the radio to under the passenger seat. Also some radioshack style RCA's will work just as good. Rockford is probably overpricing them for sure.
Subs, depends on your listening tastes. Sealed is usually a "tighter" bass while ported is more "messy". Sealed is good for rock, country, more vocal or instrumental music. Ported is good for rap/hip hop where the bass is crazy. But as always to each their own. Personally i don't like to leave subs sitting on the back seat, especially if people walking by can easily see it. Stuff got stole like that probably every week at my high school.