I've flown a departure to cruising level completely manually (no AP and no AT) and a few mins in the cruise (by which time I found it very tedious with people moving up and down the cabin requiring constant trimming). This was unusual, and I did it with a training captain. Likewise, I've disengaged the automatics at 20,000 for a approach into a few places.
I often fly visual approaches all manually -once on QNH with the airfield in sight. This has been mostly returning to my home base, with good weather and little other traffic.
Departures are mostly flown with the AP out but AT engaged. I'll discuss this with the other guy, and normally the caveat is that if it gets busy on the RT, then I'll put the automatics in.
Our SOPs require automatic flight at 1000ft, however, it is not frowned upon to fly the aircraft manually, if conditions permit - i.e. you are not flying into busy, unfamiliar airspace. I suppose, common sense needs to play a good part, and a good briefing (for yourself and the other chap).
As a pilot, particularly before your 6 month sim check, it makes sense to do manual flying practice.