yl0525,
Since nobody else has responded I will give it a shot. First, your problem is greatly simplified if the stayplate is also a pass partition. Then you don't need any holes for fluid flow. However, that's not always practical.
The real answer comes down to a combination of Code requirements, manufacturing capabilities, and fluid flow requirements. Normally, I would make the total area of the holes in the stayplate at least as much as the tube area in the pass downstream of the stayplate. The diameter or shape is pretty much a matter of how you make them. That is, whether they are drilled or burned (or otherwise elongated) holes. Of course you have to account for the holes in the plate efficiency calculations. I am assuming that you are making this header box per ASME Sect. VIII and Appendix 13.
Regards,
Speco