That's a good question with a very complicated answer.

You need to start out by making some basic size and geometry decisions like the top tube length and seat tube length, desired wheelbase, desired bottom bracket drop, and seat tube and head tube angles. The wheelbase will be determined primarily by the top tube length, head tube angle, fork length, seat tube angle, and chainstay length. Once you've worked out the dimensions and geometry, you'll be able to locate the BB and rear axle.

You can play around with the free on-line version of BikeCAD to see how different tube dimensions and seat tube/head tube angles affect the locations of the BB and rear axle, since they're all inter-related.

Bikeforest.com. Under the BikCAD tab, click on "Free Applets" and "BikeCAD".

Here's the BikeCAD output for my 61cm custom Waterford road bike.