It would be two separate payments. Actually, you shouldn't send your amendment until your original return has been completely processed and you received your refund. This would provide for any adjustments that the IRS would have already made on your behalf.
Depending on what you are changing, the IRS may catch it before you amend and correct the return. Also, there may be some other reason you don't receive the exact refund amount you claimed on the original filing. Bottom line, if possible, wait to mail your return to be sure you get the first full refund amount.
-------------
AMEND
Amending is done on
Form 1040X. Amended returns have
to be printed and filed by mail. It can take the IRS up to 12 weeks or
longer to process them. If you are due a larger refund than on your
original return, your amended return should only show the difference and you
will receive a separate check for it. If you owe money on your amended
return, it will show only the new amount owed, you will have to mail a check
with the return.
How to Amend?
https://ttlc.intuit.com/replies/3288565
