Do you normally edit your scripts and integrate them into your site design?
For example is your helpdesk just a theme or do you have it as part of your site so it links in and your site flows?
Personally, I prefer to have everything under the same design, the same style. Obviously for many, this cannot be the case due to certain reasons, however you really need to think about your companies image - and what type of image you want your company to have.
It is true, that many people are unable to do something like this - or do not have the funds to have 3rd party companies do the work for them, however it really is a shame when a case like this comes up. Personally (personal oppinion only, however others may agree), I think that a company image is lowered when a style or theme different to that of your company web presence is used on something so important as a Client Helpdesk.
It is very true, that with many programs you cannot integrate your company web presence while in other cases it's possible, however extremely difficult - although, overall, I think one should try as hard as they can to actually have all scripts using the same layout as their web site - to you it may not seem like a lot, however to either a prospective client or to a larger company thinking about using your service, it can make all that much the difference.