How can I express that something has been used for a while and is still being used?
…used a xyz system that has been in daily use for several years.
I'm not sure whether this expresses that the system is still in use.
The tense of your sentence is fine as it is because the main verb of your relative clause is actually "be" as in:
be in use
"Be" is a stative verb and it already means both an extended period and an ongoing action in your present perfect (have pp) tense.
But here are other things you might want to take into account:
the use of the word "use" twice, first as a verb then as a noun
the insertion of the adjective "daily"
Since you were mainly asking about the tense, I'll leave the rest for you to work out.