You cannot flush a manual transmission. There is no possible way to do it because there is no "flow" in a manual. The oil is there to lubricate the gears by just splashing around. All you do is drain the oil from the drain plug and refill it with new oil, just like an engine oil change.

Automatic transmissions use fluid flow and pressure to operate and shift gears. There are passages for the fluid to flow throughout the automatic transmission, whereas in a manual it just splashes around inside. An automatic transmission flush is performed through the fluid lines going to the cooler.

I wouldn't flush. Just drain and replace. 

There's usually no need to flush, unless it's badly contaminated.

Just drain and fill for manual transmissions.