Well it depends which route you go.. You could do it the easy way where you just connect the 2 wires on the stock harnesses for the amp, and you'd be using the new deck AND the amp together.. It's not technically ideal since you're amplifying an already amplified signal, but as long as you're careful with the volume and eq, it will sound fine..
The other route is bypassing the stock amp, which is a little project where you have to get access to it under the rear passenger quarter panel, and plug a "bypass cable" in, at which point you're just using the new deck.. That's what I did after I added my own amp/sub..
Something to note tho - the stock amp is honestly more powerful than most aftermarket decks at 20w RMS per channel.. My aftermarket deck is advertised as 45w "max" per channel, but after looking at the fine print, it's only 16w RMS.. The difference isn't that noticeable since I have the treble high and bass low on the door speakers (since I have the amp/sub), but if I was using it normally without the amp/sub, I don't think it would have sounded quite as good as the stock amp, as far as bass..
There's actually another option which at this point I wish I would have done.. And it's actually easier than bypassing the stock amp since you don't even have to do anything with it in the back.. You connect the 2 wires for the stock amp, and what it is basically, is a little device that you plug the speaker wires into on 1 end, and it has output speaker wires on the other end.. It has gain knobs for each speaker, so you can adjust the "already amplified signal" I was talking about earlier.. And then it just goes behind the deck with all the other harnesses and whatnot..
I'm now realizing you said you have the mach system, which I believe is the 1 that has a sub, and though some of this info would apply, I'm not positive about how you'd wire up that stock sub since I don't have it in mine.. But it's still a basic rundown of the options that are there with the notorious stock amp that has caused problems for many, many people lol..