Just so you know, you don't HAVE to bypass the amp, although that's what most will tell you on here.. I ran into this same problem a couple wks ago, but someone on here convinced me to hook up the 2 wires for the amp, and it sounds GOOD - definitely better than the stock system did, and anyone who's been in my truck agrees..
If you get the proper harness, there's a black amp ground wire on the speaker part of the harness, and a 12v amp power wire on the other part - you just tie the amp ground into your main stereo ground, and hook the 12v amp wire up to the power antenna wire (I think, either that or remote turnon) - and that's IT.. There's not a single other thing you have to do, compared to a normal install..
But the thing is, you're amplifying an already amplified signal.. So you HAVE to be careful with your volume/eq levels.. But if you have them in check and keep them that way, it sounds totally fine.. Then again, if you somehow slip up and turn that volume way up, I wouldn't be surprised if you blew a speaker or two, or four, lol..
But for me personally, I feel this scenario is totally fine.. Cuz I'm really particular about eq levels and all that anyways, so I enjoyed finding the "sweet spot", and there's no way in hell I'll ever blare it and do damage to the speakers.. And more importantly, it was the least amount of work compared to my other options..
EDIT: And if you insist on bypassing the amp - I'll give you a quick rundown of those options.. You could bring it to a shop where they'd charge you an easy $75-100.. And if you insist on doing it yourself, set aside at least 2 hrs, and go read up on removing the rear passenger quarter panel in the cargo area.. Before I figured out how to do it the easy way, I tried removing the panel, and it was not fun at all.. I only got it off halfway, and the whole time I felt like one wrong move and I was gonna break something.. And then when I finally exposed the amp, there was practically zero room to do anything.. I unplugged 1 of the plugs, but I literally could not get to the other plug, cuz of it being so tight.. And even if I did get the whole panel off, it still would have been hard, and I would have had to ordered ANOTHER part.. If you do go this route, and want a link to this part for $10, let me know and I'll post it.. And your other option for bypassing the amp is to just run brand new speaker wire from your deck to your speakers, and although it sounds easy at 1st, it would be the most difficult and time-consuming, cuz you'd be taking off every door panel and running wires thru the insides, lol,.