The neatest way is to connect the outputs from the amp to the radio harness speaker wires. You'll need to snip the wires from the multiplug first, but leave them long enough to rejoin if you go back to standard.
This is of course assuming the OEM stereo just outputs a full range signal x 4 and passive crossovers on the speakers do the filtering.
You don't necessarily need those big crossovers that come with aftermarket speakers. They are tuned for the speakers for sure, but in the past where there's been space issues and for the sake of simplicity, I simply put a 3.3 or 4.7uf capacitor on the tweeter. The bass speakers got the full range. Sounded better than the bulky crossovers to my ears as well.
This is a good shout actually because I've been thinking along the same lines and don't want to run wires through or fit crossovers.