Please help... File merge with numinix CSS/JS loader

[Miff]

Okay so Im trying to install numinix's CSS/JSS loader. Iv done this several times previously but with my current theme and with the new version of Zen cart and CSS/JS loader I have a single file which needs to be merged and will not work if simply replaced.
I have tried to no avail but my .php coding skills are very limited. Its only reasonably small but I would be very appreciative if someone could help me with this. If I simply replace the file then it completely throws off my css and leaves the site all over the place.

The file is located within the includes/templates/my_template/common/html_includes.php

The file with the _backup is the templates original file and the other is the one from the CSS/JS loader which Im attempting to merge.

Please help and thank you for any assistance.

[Miff]

No worries... It seems that the problem may not be with the files but with a couple of css errors which fail to minify when the module is activated.