George, ideally the $3k spouse contribution should come from your account, and the $1k from her account.
Your wife will not eligible for the co-contribution if she is not working - you may wish to confirm for yourself before forking out the extra $1k.
http://www.ato.gov.au/individuals/content.aspx?menuid=0&doc=/content/42616.htm&page=2&H2
