How to add new callings for a newly made quorum? Ex. EQ2 President.

We have 2 quorums in our ward, but I dont know how to show separate quorums presidencies.

I think you have to split the quorum first and then select the presidency from the members of the second quorum. Click on the pencil icon next to the Elder's Quorum title and you will see an option to split the quorum.

I think I did that, and the new quorum is made, but it shows the same presidency for both quorums.

Now that you have split the quorum, have you moved members of the 2nd quorum to that quorum? After that, you should be able to put the new presidency into their positions just as you would the 1st quorum.