What are the containers? small vessels?

What ever they are, you would need to add a landing gear / docking pad (if using HV) to the container and then be able to "pilot" the container to get it to dock on your tug vessel.

There are some containers available in the workshop, you will note that they have small thrusters dotted around the sides and a landing pad on the top to dock to a larger vessel

You cannot "lift" containers. You must dock the child ship to the parent ship then get back in the parent ship and fly it. You cannot fly a parent ship and "grab" a child ship. It doesn't work that way.

Small ship containers that dock with the cap ship freighter is what i have at the moment they don't have the thrust to lift and dock with the freighter from the surface even if i put landing pads on top it still wont lock on for the lift .

You can only dock the ship you're flying, and only to other things. You cannot cause another to become docked to or undocked from you.

Closest you could come is putting a cockpit on the container SV, running the carrier vessel up against its docking pad, and sitting in the cockpit to dock it. To undock it, you'd have to add a second docking pad, run a different cargo vessel/stevedore along that new pad, remove the old pad, and then sit in the cockpit again to update the docking. You would have to do this fore each SV.

Meanwhile, a full cargo array on a CV holds ten times as much volume and can be loaded/unloaded instantly over wireless. Compared to that, you may as well have a gang of dudes hauling backpacks full of cargo down a boarding ramp as use shipping containers.

Each container is 600 tons empty and has docking thrusters only had to make them that size to make my cap ships look right

generally cargo modules are constructed and docked to the carrier in space were the smaller thrusters would be enough to do so, and then never undocked. You wound then have a dedicated landing CV to ferry assault craft down to planet, support them while there and return with the loot