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If you create custom theme - please read documentation about custom themes. Once you decide to customize some other behavior - we might be able to suggest to you something.
There are some customization hooks in Askbot already, but they are not yet documented, b/c it is still work in progress. There are ways to customize process of answering question, showing content related to questions and answers.
The idea is that it is best to concentrate the customizations in the outside modules, which will be imported by askbot according to the special configuration parameters.
Of course you can just fork the whole Askbot repository and do whatever you want, but in that case it eventually will be difficult to keep the two code bases in sync.