I e-filed my Federal taxes and paid the tax due online. Feds rejected it, so I'll have to mail my return. Do I still have to include a check for tax due?

I originally e-filed for my federal taxes and paid the tax due online.  I got rejected, and now have to mail my taxes in.  Do I have to add attached another check for my tax due?  If so, will I get refunded for the tax due I paid online?  When can I expect that online charge be refunded back to my account?

Thanks,