First you need to check and set the thrust, you install all the top bearing halfs and sit the crank in it, measure the thrust with a mag stand and mic. If it is not enough the trust bearing will have to be sanded. Reinstall it and check again...
Then put on the center cap with the lower center hald and recheck it. If you do not have the same amount of clearance you need to sand down the bearing top half to equal it out.
Assembly...
1. Tighten main cap bolts to approximately 10 to 15 ft.lb. to seat bearings, then loosen.
2. Tap main cap toward rear of engine with a soft faced hammer.
3. Tighten main cap bolts, finger tight.
4. Using a bar, force the crankshaft as far forward in the block as possible to align the bearing rear thrust faces.
5. While holding shaft in forward position, tighten main cap bolts to 10 to 15 ft.lbs.
6. Complete tightening main cap bolts to specifications in 2 or 3 equal steps.
The above procedure should align the bearing thrust faces with the crankshaft to maximize the amount of bearing area in contact for load carrying.
Here's an articel I found with a quick search online that may help you, it is near identical to what I do when I assemble the engines in my shop.