I already posted a reply but it got lost and didn't post (sigh)
Baka marami na ding nag reply. Anyway, let me attempt to reconstruct my thoughts.
First things first.
1. Garbage in, garbage out. Don't attempt to judge your sound system using inferior sounding sources. Ngongo your mike, ngongo your sound. Buy or rent good mikes first before attempting to troubleshoot your sound system. Or maybe, plug an ipod into the line in of the PA first then do your listening test on some music that you know what sound it should be like.
2. How big is your church ? If its a rectangular or squarish hall, then you got a rather typical scenario. If your church has high ceilings and worse, a dome, that's when things get really hairy and interesting
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3. Keep your speakers as far away as possible from the walls or corners. Reverberations and bass accentuation happens when the speakers are near hard surfaces.
4. If your guitar and bass amps are to hit the public directly from its own speakers, elevate them, otherwise reverberations from the floor may muck up your sound.
5. Try to test the acoustics of the venue when there are people (and preferably typical capacity) around. The venue's acoustical response varies very differently if its empty than when there are people.
6. In a typical, relatively large Catholic church, there are 2 common approaches(afaik) to sound reinforcement. One is to use a central speaker array located at the ceiling, pointing down at the crowd. This constitutes a "point source" and will solve some of the reverberation problems. The second approach is to place many satelite speakers across the church, set at low volumes each. This will ensure that the crowd will absorb the reverberations by acting as dampeners. The low volumes per speaker will ensure that reverberations will be kept to a minimum. Hence if you church has a high ceiling and putting several satellite speakers is out of the question budget wise, you might want to "hang" your 2 PA speakers from the ceiling using steel brackets.
7. Look into purchasing a BBE Sonic Maximizer. This increases intelligibility by adjusting the phase of the sound, delaying the bass so that it arrives "everywhere" in time with the treble. High frequencies propagate slower than low frequencies.
Fix the more urgent problems first, then worry about the knick-knacks of how to route your signal.