How can I simulate the audience
already being there? Is there anyway I
can anticipate it very well?
Simulate, you can't. Anticipate, you can.
Rule number one: use your ears. Always. During the soundcheck as well as during the concert. This is a general rule that is not specifically related to your question, but you can't solve the problem as soon as you stop listening, so I just mention it.
Two major things happen when the audience comes in:
The acoustics change. Especially when there is no carpet on the floor, the effect could be phenomenal. Expect a decrease in reverberation time, so - while soundchecking - accept a bit too much reverb, then you might get clean when the audience comes in. Especially on instruments that have a omnidirectional pattern (i.e. little directionality) such as a piano or a timapni. These instruments are more liable to change in these acoustics than for instance a trumpet, that has a very directional pattern.
The noise level increses dramatically. People breathe. People move, and people... well, are living objects with all kinds of processes that produce sounds. We are never aware of this, but especially when putting many people together, this is a major change in the situation. What happens?
- There is much more noise, so there will be more masking. Masking kills high frequencies first, so make sure that there are lots of those present during the sound check.
- Human ears adapt to the amount of 'activity' where they are. This might mean that you perceive the sound weaker / less loud than you do in an empty hall, and you can hear more dynamics in a silent church. Just leave some headroom so you can actually pump up the volume a bit more, and keep a compressor on standby so you can squeeze the dynamic range a bit if things are getting to loud.
With these facts in mind and a bit of trial and error (it really depends on the location, every church is different), you should eventually find a good way to do this.