Churches are notoriously hard to get right due to the huge differences in brightness to the stained glass windows and those dark shadowy areas.
If you're not shooting people then the best bet would be to get the camera on a tripod, shoot one frame for the glass and one for the interior and put them together afterwards.
If this isn't possible then set the ISO rating as high as you dare (to aviod noise and allow a small enough apeture for a decent depth of field) and shoot bracketed frames so you can choose the best compromise for the light and dark areas.
Good lighting is essential, so try and go when it's sunny, and obviously several visits might need to be made at various times of the day to get the sunlight coming through the stained glass windows. A monopod/tripod will help, but ask if they'll be ok to use, otherwise just try out the higher ISO settings.
If you ask the vicar/priest/chaplain etc., they'll often advise when there'll be fewer people about. They might even say that you could make an appointment and they'll open the church for you and give you a "tour" and some historical info (if you like that sort of thing), a small donation to the church would be nice gesture if they do that, but up to you.
Generally don't photograph people in there if they're praying or in a service.
I've a planned shoot at the Roslyn Chapel near Edinburgh, featured in the Da Vinci Code book and famous for its incredible architecture and stonemasonry.
The shots are to be used by the Da Vinci Code Forum.
It's a good idea to contact the venue first to ensure photography is allowed (it isn't in all cases) and when they can expect you.
I found out at this venue that tripods are not allowed as it is now extremely busy due to the attention generated from the book and the impending film!