You could try using the
Solid Element Operations to notch your trusses.
AFAIK TrussMaker is one of the most versatile options for creating custom truss structures. Do you have a screenshot to illustrate the problems that you are having?
David Larrew, AIA, GDLA, GSRC
Architectural Technology Specialist
a r c h i S O L U T I O N S
WIN7-10/ OSX 10.15.7
AC 5.1-25 USA