Yesterday I e-filed both Fed & State returns. Today I had to amend my State return. Will the IRS be aware I amended one as the refund amount changed?

If you only amended your State Return, the IRS will not be aware of this. You will need to mail in any Amended returns you prepare, they cannot be E-Filed. 

Your State will process the return you E-Filed separately than your Amended State Return.  You should wait until your original return has been processed and you receive the refund before filing an Amendment to avoid any confusion.