yes you can file using the desktop app but you must enter any extension payments in the Tax Payments worksheet. The extension form does not need to be included in the e-file. In fact, the only way to include it would be to print it out and mail it in with your return.
if you want to verify that the IRS got your extension you can get an account transcript online at the IRS website.
The transcript will be list as code 460 with the due date of the return and the amount of the extension payment if any.
https://sa.www4.irs.gov/secureaccess/ui/?TYPE=33554433&REALMOID=06-00008e4d-63f6-1187-a229-7c2b0ad00...
