You can amend even if you filed your original return with a different service provider. Since ExpressTaxExempt won't be having the information you would have provided on your original return, you only have the option of amending the return through a form-based filing.
Before you begin to amend make sure you have all the correct figures as reported in your original return. This will help you avoid unnecessary rejections from the IRS once you transmit the amended return.
Currently, this option is available only for 990-EZ returns.