One thing I like about linking two enclosures is that it allows you to create two distinct climate zones: one hot and dry and the other cool and wet. If you decide to stack them, I'd make the top one hot and dry. Put your heat sources up there. Use paper or repticarpet as your substrate. In the bottom one, I wouldn't put any heat and I'd use a good humidity holding substrate. That would give your carpet a lot of options to self regulate and encourage her to move throughout the enclosure.
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