In almost all lab tests of composite aircraft structures, the boundary conditions play a crucial role. This is important in developing algorithms for SHM applications.
How we can ensure we are close to actual scenario in a test?
If you can afford to analyze the system, check if the failure modes and responses of the full system and the test specimen (portion of the system) with its boundary support conditions under given set of loads or input forcing are same or similar. If not, optimize the geometry or support to match these. In structural testing it boils down to ensuring you get the correct compliance at the support. With SHM there may be other issues besides support compliance. For structural testing there is prior literature on this topic, look for "experimental and similitude". Perhaps this can guide you.
It may be very difficult to exactly regenerate the BCs of actual structural tests. But there may be some techniques which may help to recover this information using some basic calculations. E.g. It is often very difficult to recover the actual BCs of a very basic structure like Beam. However, experimental deflection (for example at center of span of the beam supported at two ends OR at the tip of a cantilever beam) under some known load and the use of simple equations of analysis of beams may help to recover the end fixation coefficient (which will lie b/w simply supported and fixed end beam). I hope this helps.
Bounduary conditions depends on what in fact you want to investigate. You have to remember that in structural testing we almost alwas have more stiff structure. For example, testing of complete aircraft requires attachement "to the ground" what certainly has effects on some areas of construction. MOST IMPORTANT is to keep correct static scheme (also good discretization of forces) what leads to correct stress level of load bearing components of structure. In case of separate elements tests (e.g. wing) problem is easier - you have to make the most stiff conection as you can (with respect to statics of connection). It assures that eventual failure ocurrs on the tested structure, not on test rig.
For your applications (I mean SHM) you have also to remember that sometimes even ideal bounduary conditions doen't lead to correct stain/stress distribution. For example if youare testing only one wing you cannot get records of unsymmetric load what might have significant impact for e.g. strain gage monitoring system for section forces and moments determination during flight.