Can payment for amended return be taken from my refund amount. Or do i have to pay amount before amended return can be sent in.

ALL amended returns MUST be mailed in and NO the cost of the TT program cannot be withheld from the refund if you had to upgrade to complete the 1040X.  AND you cannot mail in an amended return UNTIL the original return has been fully processed  AND you have the original refund in hand.   Until that happens you do not know what you need to amend since the IRS catches some errors automatically ... so sit tight an wait. 

If the return has been processing for more than 21 days then you can call the IRS …

Call the IRS:  1-800-829-1040  hours 7 AM - 7 PM local time Monday-Friday

When calling the IRS do NOT choose the first option re: "Refund", or it will send you to an automated phone line.  

So after first choosing your language, then do NOT choose Option 1 (refund info).  Choose option 2 for "personal income tax" instead.

Then press 1 for "form, tax history, or payment".   

Then press 3 "for all other questions."

Then press 2 "for all other questions."  It should then transfer you to an agent.

Or you can contact your local IRS office.  See this IRS website for local IRS offices - http://www.irs.gov/uac/Contact-Your-Local-IRS-Office-1

If it's been more than 90 days since the return was accepted  then you can ask for help from the Tax Payer Advocate office:

At the following IRS website, find the USA map and click on your state, and it will give you the number of your IRS Taxpayer Advocate.

http://www.irs.gov/uac/Contact-a-Local-Taxpayer-Advocate

If you are unsuccessful with the Taxpayer Advocate for your area, you can also try the special IRS phone number for the Taxpayer Advocate Service at 877-777-4778.

More info on the Taxpayer Advocate Service:
http://www.taxpayeradvocate.irs.gov/about/who-we-are

http://www.irs.gov/Advocate/Taxpayer-Advocate-Service-6

Also see this article for more info on how the Taxpayer Advocate Service works:
http://www.irs.gov/taxtopics/tc104.html