Which model crossover are you using? That affects how you'll have to connect the inputs. The outputs will be pretty much the same regardless of what kind of crossover it is. Connect the front channel outputs of the crossover to the front or number 1 channel input on the 4-channel amp. Then connect the rear channel outputs of the crossover to the rear or number 2 channel inputs on the 4-channel amp. You can hook up either the 6.5s or the 5.25s to either the front or the rear channel speaker outputs of the 4-channel amp--it's up to you, although I'd probably hook the 6.5s up to the amp's rear speaker outputs. This manual might help you a lil bit if you get confused.
If your crossover has a subwoofer output, you wanna connect that to the inputs on the 2-channel amp. If it doesn't have a separate sub output then it kind of defeats the purpose of having a crossover. Technically you could still hook it up but it'd be a bit more complicated and you'd never have as much control over the sound. So I'll just assume that your crossover has a subwoofer output, and I'm also gonna assume that your sub is a 2-channel amp, and thus these instructions below only apply to a 2-channel amp.
Regardless, you'll connect the subs to the speaker outputs of the 2-channel amp.For the subs, wire each sub in parallel so that the 2-channel amp will see a 2-ohm stereo load. So basically one of your subs will be for the left channel, and one of them will be for the right channel. All you have to do is connect the positive for the left channel to both positive terminals for your first sub. (remember cuz this is a DVC sub it has two sets of speaker connections on the sub). Similarly, you'll connect the negative for the left channel to both negative terminals on this sub. Then repeat the process, but this time use your other sub, and the amps other channel.
I would recommend a separate line output converter rather than use one that may be built in to the crossover just cuz sometimes using the built-in ones can fry your factory radio. All this converter will do is change your factory head unit's speaker outputs to an RCA type line-level connection for use with the crossover.
important note:
Use the head unit's front speaker outputs to connect to the line output converter. You'll need to cut these wires, and once you do that you'll be left with two ends for each wire. One end leads to a speaker, and one the factory head unit. Whatever you do make sure you don't run speaker wires from your 4-channel amp's output to the head unit's output. So once you cut the wires you're not gonna ever need to connect them back together. Just go straight to the speakers themselves.
Sorry this is probably kind of confusing but I really suck at drawing so this is the best that I could come up with (as opposed to a diagram).
Let us know how it turns out and if u need more info, as this is just the basic stuff.