Changing transposition whenever the instrument changes?

I'm currently writing the orchestral score for a musical I've been working on, and since the first performance is coming up I'm tailoring the orchestration for the ensemble we have. It consists of Reed (piccolo, flute and alto flute), Drumset, Percussion, Piano, Synthesizer (using a variety of instruments like clarinet and glockenspiel), guitar, two violins, and bass. My issue lies within the synthesizer. When the synth part needs to change to a different sound, I use the 'Instrument' feature to do it. However, when I change to a transposing instrument, the part transposes too. I figured the way to counter this would be to transpose the part in 'Staff Properties', but it seems to be transposing the actual 'synthesizer' part as opposed to the 'clarinet' parts which is changes to. I've attached an excerpt from the Overture, which demonstrates the process and the issue (It's still a work in progress so forgive the dozens of empty measures and non-finished parts). Also, the concert pitch button works, but then messes up the other parts, like the piccolo part, because when the piccolo switches to flute it gets all disoriented.
If anyone knows what to do, it'll be a big help. If you have any questions, I'll try and provide more info.