Questions on an upgrade.

So just bought a 2010 Access Cab Tacoma. Cant stand the stock audio but my funds are rather limited. I got a decent deal on a Pioneer HU and a pair of Pioneer 3 way 6x9s. Not high end at all but it should be a decent upgrade, I'll add to it and upgrade more later

I have a few issues that I need some advice on.

1st are these idiotic speakers in the headliner. I don't want to remove the headliner but i don't want these speakers connected after i upgrade. I was hoping to disconnect them but i cant seem to find any info on it. Anyone know which wires these are? Will there be any issues disconnecting them? Will I get decent sound with just the 2 6x9s? No place to but speakers in the access door without some modding that I'm not ready for.

2nd there is a horrible factory sub between the the back seats, I'm going to replace it later. I've seen a lot of different options for subs but I read that there are holes after you remove the factory sub. Has anyone seen a box that will have a similar look or placement? I realize it will limit the size of the sub but I'm not looking for anything massive. I'd like to keep a factory look as mush as possible.

Didn't know I'd need any kind of mount to get the 6x9 in the doors, speakers are going to be in tomorrow. I'd rather not order something online and wait (got a day off). Any brick and mortar stores that would have a suitable mounting kit?

Thanks for any help