OP use the xovers on the HU. As far as where to set them, start by unhooking the rca's to your highs amp. Now turn up your HU to the loudest volume that you'll listen to, usually around 70%, and adjust the xover and EQ for the cleanest bass obtainable. Take your time. Try all the LP xover points while adjusting the low end of your EQ. You may find that a higher LP xover setting(80Hz) with the EQ in those frequencies turned down sounds better than a lower LP xover setting(50Hz) with those frequencies turned up on the EQ, and vice versa. Do this on all types of music you'll be listening to and try to find a happy medium.
Now for the highs. Pretty much the same procedure. First hook your highs RCA's back up. Now either unhook the sub amp or if your head has the function, turn the sub output off. Adjust your HP Xover points and EQ to obtain the best possible sound at the same source volume you set the subs at. Try not to adjust the EQ frequencies below that of your HP xover point as they will effect the sub stage you just set. Once again, take your time. Adjust everything till it sounds clean and the way you like it. Once the HP is set, you may want to go back and slightly tweak the LP again if you adjusted the EQ much on the low frequencies while tuning the highs.
Now, once both HP and LP are set, turn your sub amp back on and blend it into the highs at volume using the sub level adjust on your head. Tune it the way you like it. If you decide to play with the bass boost or other settings like that on your HU, do so in moderation and maybe turn off each amp like above so you can hear what that setting is actually doing to your speakers.