Yeah I can't really tell what is going on from that pic, but I'll give you what I know.
Also, what do you mean by, "when I hit remote?"
The main wires coming from an HU, after all your conversions have been made should be:
Some RCA's, 1,2 or 3 sets - looks like the connector box you've been talking about takes signal from the speakers and out puts RCA signal - right?
Some speaker wires - 2 or 4 sets usually gray, green, purple, and some other color with a stripe down one of each color to differentiate between positive and negative.
The main power wire - usually yellow. This is where you're HU actually draws current. It is always live, even when you're car is off, that's why the clock still runs.
The "remote wire" - red wire that goes live when the car is turned on. It is a signal wire and nothing more.
The ground wire - black wire that runs to a ground some where in your car.
The last three are usually bundled close together. (power, remote/"signal," and ground)
You need to run a wires from your RCA's and from your remote (red) wire back to your amp.
BTW, what amp do you have?