Library or include

I just picked up a site was created in Dreamweaver. It currently uses many of DMX2004’s feature most importantly templates and library items. My issue is with the library items. I don’t see the point of them… i would like to switch these over to server includes. However, these library items contain conditional statements designed to work with the templates… when I include the file rather that have it as a library item, the conditional statements are not interpreted. Is there a way around this?