When using Malphus, use him like you would use Brain or Bolt on the surface, as they are all looters. Malphus's greatest asset is his ability to jump over walls, thus helping him get to the the resources. He can also be used as a minesweeper because of his great speed and cheap price.
When defending against attacks with Malphus, keep in mind the fact he can jump over walls. Often, a player will surround a Resource Pod, Storage Silo, Town Hall and/or Under Hall with walls, and put towers nearby, thinking it is safe. But many have learned the hard way that while the towers are distracted by a mob of tank monsters such as Ichi, Crabatron, Zagnoid, or Gorgo, Malphus can come in and obliterate their Town Hall, Under Hall, Resource Harvesters and Resource Pods, and not have to worry about the walls. Mines can be used to kill Malphus effectively, as they have low health, and if you can afford it, King Wormzers, Grokus, Balthazar in your Compounds, or fairly powerful monsters in your bunkers can kill off any Malphus that get too close.
When attacking with Malphus, never send them in first, or alone. Malphus has low health, and will not attack towers until the last Resource Pod, Resource Harvester, and Under Hall has been destroyed, and by then the towers would of finished them off. Malphus works very well beside tank monsters, such as Zagnoid, Crabatron, D.A.V.E. or Gorgo as they go for the towers as Malphus loots all the other buildings with ease.
It is not suggested using Malphus as a bunker monster, because of his fairly weak stats, and although he can jump over walls, using Rocket D.A.V.E.s, Crabatron, or Balthazar would be a better option. Malphus is also not recommended as a Champion killer, as he cannot attack Fomor, and can be killed easily by either Gorgo or Drull.
I recommend you to use Malphus into box yards and those bases that are easily to farm.