wait until the IRS finishes processing your original return. This is what the IRS prefers. filing an amended return before this is done can create issues and actually delay your refund. in some case the IRS automatically makes the correction and does not need or want an amended return.
if you asked for $10K back and the IRS corrects this to $9k that's what you'll get so there's no reason to send the IRS a check for $1K. also since you are still getting a refund there should not be any penalties
