Here's what I do:
1. Turn the top wing upside down, cover it with a piece of tracing paper, then mark the location of the strut attachment points.
2. Glue wing struts to the bottom wing and cabane struts to the fuselage. Using whatever I have on the work bench to build a temporary jig, I suspend the fuselage/bottom wing assembly over the tracing paper, making sure everything is square, even, and lines up with its associated mark.
3. When all the struts are set (but not 100% permanently set), I set the assembly into the inverted top wing. Sometimes, I need to work on a strut or pair of struts at a time to get everything perfectly lined up. When I'm happy with the fit, I CA each strut into the top wing.
Just my way of tackling this problem. Others may have ways that work better for them