We use the verb "to use" when we are interacting with the item in question. So, we would say,"We use our computer every day." We use the verb "to run" when the item in question does most of the work itself" For example we would say that we run a machine. We are only there to supervise the action. The machine is doing the actual work.

I use my computer every day I run my computer every day

You need to give us the sentence which confuses you. As Jmat has said, these are different actions.

In what context are you confusing them? They're completely different actions.