Since there is a Half-Troll template in the Fiend Folio, I was wondering if that template could be used to make half breeds of the various Troll sub breeds? Such as the Crystalline, Cave, Forest, Mountain & War trolls found in the Monster Manual III? Or is there perhaps another template or set of templates I need to look at? 

And if I did use the Half-Troll template, What would be a good and balanced way to show that this particular Half-Troll is descended from one of the sub breeds rather than a normal Troll?

It's not so much that the template is unclear as it seems to assume a standard set of abilities for a creature descended from a whole host of different iterations of the troll, which each have a few different abilities than the rest. Some abilities are indeed going to be standard but it's those "others" I'm curious about. It mentions that a change has to be made for the Scrag (Aquatic Troll) for instance, which leads me to believe that other sub breeds would "possibly" require alterations as well but doesn't make mention of any of the other types

It's possible that, much like the Half-Dragon template, there's been an updated version printed in a different book that I'm unaware of. I just mainly want to make sure that the Half-Troll template presented is, by RAW, useable with the sub breeds