I do not know of any other way to make changes like this in a template file. It may be worth having a copy of the page detached from the template, then add in the progress bar and copy and paste the code that is added into the correct spots in the template derived file.
The progress bar should only be adding in code like this in the head:
<script src="WA_DigitalFilePro/jquery-blockui-formprocessing.js" type="text/javascript"></script>
And like this in the body:
<div id="form2_ProgressMessageWrapper" class="blockUIOverlay" style="display:none;">
<script type="text/javascript">
WADFP_SetProgressToForm('form2', 'form2_ProgressMessageWrapper', WADFP_Theme_Options['BigSpin:CaboSunset']);
</script>
<div id="form2_ProgressMessage" >
<p style="margin:10px; padding:5px;" ><img src="WA_DigitalFilePro/images/cabo-largespin.gif" alt="" title="" style="vertical-align:middle;" /> Please wait</p>
</div>
</div>
