First things first, use your crossover. You should connect your main outputs to it and feed your main loudspeakers and your subwoofers power amps from it. Connecting and learning how to configure your crossover should be easy enough and straightforward, after you do some reading of the manual. This will give you the advantage of using less faders to control the total volume and you can set the main/sub balance from the power amps gain control. Then you will also be able to tune your system more efficiently using your main out parametric or graphic equalizer, since the changes you make there apply to your whole system, excluding the wedges. And probably the acoustics of your new church will demand tuning on the frequencies below 200Hz. If your crossover allows it (extra pairs of output), I'd recommend feeding your wedges from the same output you feed the main loudspeakers, which will give more controlled low frequencies. If that's not the case or if your monitors need drastically different equalizing from your mains, use the same post-fader technique to remove the same frequencies that you set you crossover to remove from the main speakers and apply further equalizing, according to their special needs.
Then, as @audionuma suggested, don't use your headphones for the tuning of the system, use the system that needs to be tuned. Use your ears and move around the place to check the sound, since it changes a lot from place to place, depending on the placement of the speakers and the acoustics of the church.
Now, which kind of EQ you choose to use depends on the needs of the tuning. GEQ should be enough for the most of tuning and getting rid of ringing/feedback. Parametric EQ has less bands, but allows you to shape the filters response with much more options, so you could use it for example to boost the highs all together, instead of boosting all the bands of high frequencies of your GEQ. Also depending on the kind of music/sounds that your system is going to be used for, you should apply a low cut, say at 60Hz, since probably you are never going to need these frequencies for any reason. If for example the system is going to be used only for a choir, you can apply the low cut at 80Hz, or a little higher (again, listen to it), and with this you are going to get rid of a lot unnecessary rumble and your power amps are going to work more efficiently, since these frequencies are power demanding. For music with heavy bass and a lot low end information, the filter should be set at 40hz.
Try before applying drastic equalizing to experiment with the placement of speakers and, if any, your microphones. A lot of problems can be avoided this way and it will allow you to use your EQs mostly for enhancing the quality of the sound, rather that fixing problems.
