Well, difficult job. I cannot say I am an expert on these questions, but I have some limited experience. Here some generic suggestions when placing a virtual organ into a real church.
1) Consult the textbooks of acoustics of the organbuilding to determine the size of the virtual organ suitable for your church. There are rules to follow when determining how large the organ should be to suit psychoacoustically the venue.
2) Use as many speakers as possible. You will like to use at least two pairs of speakers for each division. Why two pairs? The speakers have rather limited directivity in emitting the sound. Pipe is emitting the sound more evenly into the space. Therefore, we found out in practice, that it is worth doubling the speakers, each heading in different direction (like 90 degrees apart or so), or some speakers heading upwards, some to the front, it needs experimenting. Well, a cheap trick but it is prooved that it works... Another option is to construct a completely multidirectional speakers. This is probably the best choice for a church installation of a digital organ. There are working designs of multidirectional speakers available on the Internet.
3) if you have even more speakers, then use the more, splitting the ranks among the speakers. Trial and error will be necessary to determine the best results. For example, if there are two 8 feet ranks, I would send the first one into one pair of speakers while the second into the other pair of speakers.
4) Always use only the dry sets. Even where there is little reverberation, the dry sound is suitable, since when used for accompanying another instrument or a congregation; weird results would be obtained with the wet sound: the congregation or a violin would be heard without reverb, while the organ would have the reverb from the speakers... And even using "wet" sample set with their release tails cut does not help, because the result would always sound "muddy". Always look for DRY sample sets for a church use.
5) Well, some would be tempted to say that dry organ sounds awkward. It is well known phenomenon and the textbooks on the organbuilding acoustics say that organ sounds convincing if placed in a room with at least 2 seconds of reverberation... Well, if you do not have it in your chapel, then there is no help. If you would build a real organ in that church, it would have no reverb anyway. The only possibility to get the most out of the sound is smart voicing. I know from the experience, that even organ in a dry environment can sound well if voiced with attention. Every stop then needs real strong character to please the ears of the audience. The chiff must be expressive and the higher harmonics and high pitched stops must be in balance with the lower, the organ must be less shouting, while sound more tender overall. A lot of work, but rewarding. In a reverberant space, almost all the voicing errors are masked by the reverberation...
6) Always try to place the speakers as high as you can. Look to the example of real organs, they are many times seated very high up in the church, some divisions right below the ceiling. If you can reach that height with the speakers, give it a try.
Also, you may try heading some of the speakers not to the public, but to the ceiling or in other direction to obtain special spacial effects. When we made a sound tests in a big church in Prague, we found out that positioning the speakers near the ballustrade of the organloft was producing bad sound. When we positioned the speakers more to the back of the organloft, the sound was more natural. Remember, that pipes in real organs are distributed among several (or many) divisions, which are spaced in various interesting ways. For example, an Oberwerk speaking from very high, Positive speaking from the ballustrade, Pedal speaking from sides of the church, etc. You need to be creative in the speaker placement, to achieve some acoustically interesting spacing of virtual pipes and divisions in the church.
7) I found out that it is often necessary to boost the high frequencies very much when using speakers (monitors), I am not speaking now about the PA boxes! The high frequencies disappear very soon in normal speakers since they are usually made for a short distance listening. Hence, you need to boost the heights enormously (12 dB is not much in these cases sometimes we went to almost 20 dB on high boost! Well, of course we blew up the tweeters very soon, but this is the life, the replacement tweeters are not that expensive) to get the natural "air" hiss through the pipes. If using PA boxes, this problem disappears, because they are made to bring the high frequencies to a long distance. However, new problems appear, because the cheaper PA boxes (you do not want to spend thousands of EUR on the boxes, because you will need a lot of them) are not well frequency ballanced and usually have also other limitations (no bass response, for example). You can measure the response of the speaker and make special filters to balance the response. It is necessary to create a convincing pipe organ sound.
8) Be ready to voice the virtual organ a lot. The sample sets are ready for acoustically perfect "environment" (such as headphones, or well treated rooms). When using the samples through the speakers in an environment which is not acoustically perfect (also in many living rooms!), you will have to voice. It is then as if you were given the rough pipes and these always need to be voiced for the given space!!! Look what is happening with a real organ: When a real organ is moved from one church to another, it always needs a careful revoicing by the organbuilders. You will be the organbuilder for your virtual organ in this case! That is really a creative job which I myself love.
However, the result may sound very different from the original organ. That is normal. The character of the organ will change with the church. When we installed the Freiberg dry sample sets in one church in Prague, we had to revoice it a lot: and when we arrived at a sound which was convincing for the given space, it did not sound as Silbermann, rather, it was more like a symphonic organ. But the most important aspect was that it sounded convincing, as if real pipes were used. The mixtures had to be attenuated, while the large pipes needed boosting, also the high pitched stops needed to sound more transparent (i.e. reducing overall volume while boosting higher harmonics).
9) Be ready that the organ may not sound convincing in all spots of the church. This is normal, every space has its "sweet spots" and also the bad ones.
Well, to voice an organ is a real art. Organbuilders must be very experienced to achieve well balanced sound in the given space. Do not expect too much of yourself if you are not trained expert in organ voicing...