O.K. your post is a little confusing, so let me sort this out......
1. Your harness has 2 blue lines..... one for power antenna, and one for power amp turn on. Make sure you have the right ones going to the right ones, as the antenna line turns off when you switch from tuner to any other source.
2. If the blue lines aren't fused, then there is an internal overload protect. In other words, if either of the blue lines has more than half an amp on it, the protector kicks in and cuts off the 12 volts going to the line. Check for shorts and over current draw.
3. Of course, check all grounds. That is the most important, I cannot stress that enough. ALL grounds in the system, amps, speakers, head unit, etc.
After that, post any other problems and we'll try to walk you through them.