So you want to keep the factory amp? I wouldn't suggest that. I'd recommend getting rid of the factory amp altogether, they're usually not the best, and it would be difficult - if not impossible - for them to work together.
I google'd for a quick sanity check and I'll post a snippet from WikiAnswers:
I wouldn't...first most after market amps require a certain amount of power for proper function, such as a good ground, a good power source, some sort of RCA audio input, and a remote turn on. I know trying to figure out the same thing once. Plus most factory amps are just a plug of 16 gauge wires, and by time you through all of them to figure out power,ground,and remote, you still have to figure out how to send and input to your after market amp. Lets say you did do it and figured it all out, once you turn your deck on the after market amp probably would go right into protect due to not having enough power...
Even if you wired it up right I have a good feeling it wouldn't sound good. One exception I can think of is that some amps have a type of 'line out' where they directly support daisy chaining to additional amplifiers. Typically the amps have to be the same model/family to work in this manner though, to sync the power being delivered to the speakers, and other low level audio/power stuff that's currently beyond me.
For a solution though, If your factory unit has Pre-amp outputs, then you have your answer: Run a pair to your aftermarket amp, and you'd be good to go. If not, then a line-level converter is the route you'll have to go.
You definitely want to use the low-level (RCA, pre-amp) outputs from your factory head-unit if available. That way you don't get amplified noise from your head-unit, which goes to your shiny new amp that you can't crank up because it will start to clip at a very low level. That way, you get an unamplified signal going to your amp, which is precisely what it wants.
YMMV, but I know older factory head-units don't have pre-amp outputs. If it does, then awesome. You also asked for where to splice: I'm assuming that's for if your radio doesn't have pre-amps. However you said your amp has high level inputs, if that's the case then there I would splice close to where the amp is going to go, this will minimize or eliminate more splices. Typically the connectors that come with amps for high level input don't have a lot of wire on them(see below), so you'll have to splice close to the amp, and since you're running all new wire you can run wire straight from your HU right up to the amp and splice there.