From you fitting and desired dimensions the frame builder will do a bike drawing with all the angles, lengths and details. For me the first proposed stand over height was a touch taller than i wanted, so they put a little slope in the top tube. The builder proposed a stem length and angle, at the final fitting the shop put on this suggested stem. Rode it on the trainer for a few min, swapped the stem for one with a slightly different angle. Then went for a real ride for half an hr or so, when I got back to the shop, asked to have the first stem installed. Have changed the stem twice since then, currently back to the original. The fit and bike set up i ended up is perfect for my needs - the LBS and frame builder did a great job translating those needs into frame and bike build. Glad i went the custom route.