I can't get the portal thing to work

I create an engineer, and move him (or it) to the portal. The engineer than breaks into pieces. What should I do to enable that portal?

You capture buildings by moving engineers to the small control tower buildings next to things like the portals. The red arrow-creatures moving along the ground are viruses, and will try to destroy your units. It sounds to me like you have just moved an engineer straight in without destroying the viruses beforehand. Try creating a squad and destroying the viruses around the control tower first.