Ok,..I think in the real world its great to flush your engine after every trip out, but not everyone does. If you can flush it it will just help it go on for that bit longer. But i wouldnt worry to much about it.
Im not sure that you can flush the engine when its in the water, And obviously dont trim it up to put muffs on it while the boat is in the water. (if that makes sence).
I would not worry that its not been flushed after 12 days, just flush it next time you get the chance.
Your Auxilliary, engine if it were me i would check it worked every time i went out, Which is what i do with the boats at work But that maybe me being parranoid. If the Main motor breaks then its good to know the other will start!!.
Leaving the engines for a few weeks is not such a problem. The only thing i would say is, with the Opti dont run the fuel out of it. This will overheat your fuel pump and knacker it (if you do it regularly) Its probably a good idea to get some Fuel Stabilizer and put it in you fuel tank/s This just stops the fuel from deteriating while the engines are not being used. Old Fuel can cause lots of problems.
You can buy proper Flushing attachments for the Optis which will be better than using muffs, Speak to your nearest dealer for advise on how to use it etc.
Hope this helps.