HI Alli,
Without having your actual template to work with, it's kind of tough to narrow down how you're attempting to get the results you'd like, and how it's turning sour. I'll give it a shot, though.
If you're getting repeats of your requirements, it may be that you need to use the keyword ChildRequirements in some place(s) rather than just Requirements.
Also, open up the custom reports user guide by clicking Reports / Custom Reports on the ribbon bar and take a look at section 5.6. It may just be that you'd need to individually format some nested repeat statements. Again, though, without your template it's a bit tough to tell.
If you'd like us to take a look (and keep your custom template out of the hands of the community at large), just email it to us directly at support@serlio.com. You can trust us not to share it. Or, if you don't, we can sign an NDA.