Right-click the Cover Shield ability on your bridge officer's tool bar. This will turn it red and indicate that they won't use it automatically.
Then drag the ability onto your own toolbar. Click it when you need it (for added control, put the "move to this spot" command for your engineer right next to it, so you can place the boff where you want the shield, and then erect it). It's not as neat or quick as doing it yourself, but if you're not an engineer captain it's better than nothing.
I'd still rather have my Engineer BOFFs doing something more helpful all the time, then have a mostly wasted ability that's useful rarely.
I don't like the mortars because they're too slow and their target selection leaves much to be desired. Then again, they could've been buffed (I gave up on them in late 2010) so take my advice with a grain of salt. When I consider what would be best in a slot, I don't think mortars really stand up to turrets or the support drone.
Mortars are great vs slow moving enemies I.E BORG, Elite Gorn. They do great damage in bursts which is perfect when combined with knockdowns and slows. If you can get mobs to mass to a single point they can be devastating since they use ae damage and can hit for 300s (or more sometimes).
I use mortars against other targets too, but some might be annoyed by the setup that I do. I place a phaser turret in front of my mortars a ways and put mortars behind and in cover if possible. The mobs run up and start shooting the phaser turret and my mortar/s demolish them. I also flank the enemies with my other doffs and myself, tends to wipe most groups out very fast and harmlessly(to my team).
I have also used cover shield on boffs but usually only on maps where there is not a lot of cover and not in restricted places, they are just too inconvenient at times to use. My typical loadout on an Engie Boff is Phaser Turret 1or2 Medical Generator 1or2 Quantum Mortar 3 and either a weapon malfunction or shield recharge.
I just used them for a ground PvP map. Mortars are awesome and they are indirect-firing. I got a few mortars up and the enemy team had a very hard time breaking through my fortifications because stand still for a few seconds and ignore the purple marker = boom.