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i keep trying to export my reports, whether in html or pdf they come through distorted where i cant read them. i believe it may have something to do with the conversion format.

A possible reason is that you have edited your report template and it causes conversion issues. If you click Help -> Send Project to support, we will be able to take a look at your template and fix possible errors.
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also, i've been trying to export to my website but would like to export it to a folder such as
http://mysite.com/reports/client_name; however, unlike when i export as pdf, i cant seem to find a function to auto add a folder. Is there a feature i'm missing?

You can find the FTP upload options in Preferences -> Publishing profiles. The "delivery option" section is the one you need.