To make everything (unnecessarily) super clear - You need a cargo rack (optional compartments). Not for the engineering materials, but for the limpets. When you have both collector limpet controller and the cargo rack on board, go to the advanced maintenance in station menu and load up the limpets.
Don't forget to put the limpet controller in your firegroups.
When on site, you have two options
1) target a piece of material you want and fire the limpet. It will go collect that thing, bring it back and self destruct.
2) Fire the limpet(s) without anything targeted. They will hang around and collect anything in their range until they run out of fuel (the lifespan of a limpet is dependent on the rating of your limpet controller).
Side note - if you want to fight while having limpets around, just remember that you need to open the cargo scoop for them so they can deliver the goods, but with cargo scoop open (similarly to deployed landing gear) your max speed is halved and you can't boost.