@justindelimo
Hello. Bolted connection is the correct way to do this, after you have built the piping with Tube & Pipe. If your assemblies are coming apart, I believe this may be due to how the piping assemblies were constrained. What you want to do is constrain your Master Pipe Run to the top level assembly using Flush constraints, origin plane to origin plane. And then, activate the Master pipe run and constrain each of the individual pipe runs to the Master also using Flush constraints, origin plane to origin plane. See my video demonstration.
This is a good practice for anyone using T&P because it "locks" you pipe runs in place so that they cannot move when working at the top level of your assembly.
Video link