I'm not really sure if I understand your question.If you're building a Hatz Biplane, you install the wings as shown on the plans which is a 25 inch positive stagger (50% chord) and 50 inch gap (100% chord). This provides a good range of CG travel, good stability, relatively good cockpit ingress/egress and good visibility from both cockpits. It also provides good angles for the bracing wires to give good strength and light weight. I wouldn't advise you to change any of this unless you're well equipped to do both the structural and aerodynamic analyses for the new configuration.
If you're not building a Hatz but are interested in designing your own biplane, I can offer a rudimentary rationale for positive stagger.
First, positive stagger causes the bottom wing to operate in the downwash of the top wing, especailly at high angles of attack. This effectively lowers the angle of attack for the bottom wing which means that if will still be flying when the top wing stalls. This produces a more gentle stall than if they both stalled at the same time and if the ailerons are on the bottom wing, you will still have aileron control when the top wing is stalled. The same effect could be achieved by incorporating some decalage (different angles of incidence between the top and bottom wings), but that produces excessive drag in the cruising regime. Positive stagger was really a clever way to achieve good stall characteristics without affecting other flight regimes.
Second, stagger increases the range of travel of the center of gravity over what woudl be possible with zero stagger. Since most biplanes have narrower chord wings than comparable monoplanes, this is very desirable, especially since most planes use tandem seating which requires a wide CG range. Randy Brooks has writtten a good easy to understand procedure for calculating the CG of a biplen with stagger, It is located on the builders page under his name if you are interested.
Third, moving the top wing forward allows the horizontal tail to be brought forward and still avoid the downwash from the top wing. This allows a shorter fuselage structure which results in less weight while still maintaining good stability.
Fourth, positive stagger allows easier ingress/egress for both cockpits.
The interference between the top and bottom wings is most noticible at high angles of attack (take-off, climb, glide and langing) and has very little effect at cruise speeds. If you're after ultimate aerodynamic efficiency, you shouldn't be considering a biplane anyway. Biplanes ruled during the early years of aviation because the provided a rigid structure at light weight. They also had a higher rate of roll due to their shorter wings which was very desirable for a fighter plane. While there have been some very fast biplanes (Beech Staggerwing, Grumman F3F-3, Laird Super Solution, Japanese Pete. etc.), it's much easier to go fast if you're only pulling one wing through the air.
If you are interested in a detailed technical investigation of this subject, there are several good NACA technical papers available. The link to their technical server is http://naca.larc.nasa.gov/
Most of the biplane stuff is found in the years 1917 through 1932.
Sorry to write such a long response to a simple question, but sometimes I get carried away. I hope this has helped.
Jim Phillips