Drupal is a content management system - it has a member base, themes, admin system, permissions and more all built it. The Mysidia script is basically the same, it has members, themes, ACPs, permissions and adoptables and all this other stuff built in. To use Drupal, you'd have to merge the two systems - which would take more time and effort then it's worth. Drupal and Mysidia are more or less the same thing. You use one or the other.
You can use a Drupal /theme/ if you want, but you'd need to rip out all of the drupal coding from it, and Mysidia breaks 75% of the premade templates out there, for who knows what reason.
I think you're better stuck with just building a template based off the mysidia templates - If I'm deducing your question right, you are new to this script, and perhaps to coding in general, since you're using drupal in the wrong context. Mysidia is designed to give you all you need to build a complete site, as is Drupal, you don't need anything more but both is too much.
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