You can certainly just use the parts of the template that are relevant for your environment. That will mainly be removing the AD components from the template and setting the parameters to your existing AD values. Be sure to update any Ref functions that refer to AD resources to what your actual values are as well, if present. You do not need to store the PS scripts in a new bucket, the default used by the Quickstart is public.
Edit: If this is for purposes of testing and experimenting, then no problem with what you are doing. For a production deployment, you may want to deploy an independent AD forest for Exchange, sometimes called a "resource forest". This article is for 2013, but the same concepts apply.
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