Troubled ferrying infantry ...

[JDR Dragoon]

So I am assuming that if I happen to have a few units which status is an engineering unit, but only acting as a mine clearing one, yet they have boats, it means they still can ferry other units in their boats, but they do not have the equipment and ability to set up a bridge,right?

An engineer unit w. boats might still be able to build a bridge provided it is capable of doing so (it will say so when you rightclick on the units information box). But it cannot do this at the same time it is ferrying infantry using the boats.

Is is also correct to assume that in order to have them employing their boats as a means transport for other units crossing, I am to place them on the bank in a deployed mode?

Basically yes. The engineer really only has to be in the same place during the ferrying and not do anything else (I think it can Dig In though). It doesn´t have to do anything. The unit being ferried is the only one active.