Relative pathname problem with subdomain

I’m not sure if this is the right forum to post this in. I just discovered that admin.site.com/../ and site.com/admin/../ are not the same. At the moment my client can use either but when he used admin.site.com none of the relative pathnames on the main domain work. Some of the files are on the main domain and i dont know how to access them.

Thanks,
Brendan