The facilities seem to be housed in large industrial buildings; the facility in Young Bloods was in an Earth factory.
Victims are kept in a holding room before being taken to a harness chamber in the main part of the facility. The harnessing chamber seems to take up much of the building or is at least the largest room in the building.
The chamber has a large tank in the center which houses the harness creatures prior to implantation. It is surrounded by metal slides which are used to lead the creatures down to a victim. It is unknown if this is part of the tank or re-purposed earth technology. Unharnessed children are placed beneath the end of these slides; strapped down onto gurneys with their backs exposed. Once a victim has been harnessed they are moved to one side and left until the harness has presumably taken complete control of the victim.
While heavily guarded on the outside to deter human exploration or rescue attempts the location has little to no guards inside. Only a single Skitter was seen overseeing the attachment process and the rescue team was able to enter and escape with little resistance. It can be assumed that the lack of internal guards was the result of the aliens belief that human would never come across the place or be deterred by the Mechs guarding the entrance.
A harnessing facility was discovered in the episode Young Bloods being heavily guarded by patrolling Mechs but its true nature was unknown at the time. It was only after Diego's group was captured trying to rescue their friends that the area was explored. The mission was personal for Tom and Weaver who both had children trapped in the building awaiting harnessing.
While Maggie and Tector rescued the children in the holding room Tom, Ben, Hal and Weaver stormed the harnessing chamber to rescue the other children before it was to late. Fortunately the inside of the base was lightly guarded and the humans arrived in time to save Matt and Jeannie from being harnessed. After killing the harness creatures that were trying to attach to their children they removed their restraints and grabbed the few harnessed children they could carry to take back to have the creatures removed. While the initial plan was to simply escape they ended causing damage to the facility when Ben shot the tank holding the harness creatures after one tried communicating with him. The humans shot all the creatures before making their escape but one bit Weaver on the back of the leg and put poison into his blood stream that later almost killed him.