i put my regen effect on lvl 1 but it heals me like if i had regen lvl 1000 or something

Can you post screen shots?

In the first image, if you use the "Cooldown" method, it will need to be on the trigger "When Right click on block" or some other trigger that is not on a Update Tick, because that will trigger the Cooldown constantly.

On the other hand If you want it to give you regen but only after a cooldown under "Flow Control" there's a block named "Wait # ticks on server-side" with this you can use a Logic NBT tag on the player and check if its true/false and use the wait block to set it back to false after the wait.