I also suspect you may not have run thru all the SC nonresident Q&A yet. While you are preparing your Federal tax return, the SC tax return assumes most of your combined income is SC-taxable.
BUT, after your Federal section is fully filled in (every scrap), you'll go thru the SC Q&A and need to indicate what sub-portion of the Federal $$ are also SC $$. For you, that's likely only your SC wages.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
