Hi Ryan,
I did a quick test this morning in my own Method account, mimicing what you are trying to do with your cases and Contacts Portal. I logged into my Contacts Portal as a test Customer, went to the Customer Service tab, then clicked the "Question" button. I filled out all the necessary fields, after submitting my question, my new Case then showed up in Method. I logged into Method, went to my Cases tab and pulled this case up. I added a new Activity to this existing case, saved it then switched tabs back to my Contacts Portal. I logged out/in just to be safe, I then went back to the Customer Service tab, my new Activity was saved, and showing up in my case notes in the Portal.
I believe what I mentioned above is along the lines of what you are attempting to do. Can you please confirm you didn't miss any details, like making sure when updating the Case in Method, you made sure to click save for Activity AND Case? You confirmed you can see this new Activity in Method after adding it, do you see it in the Case notes, or will you see your activity comments from a grid/or within the new Activity?
In regards to your Custom Email Template not showing in your dropdown, please make sure you haven't selected the "hidden" checkbox for this email. To confirm, go to Home->EmailTemplates, then load your CRM_Caseupdatefor_Customer Template. On the right-hand side, directly above the "Category" label, you will see two checkboxs, "Is Active" and "Is Hidden", make sure it is set to active, and that it is NOT hidden (you can hover over the is hidden label for a definition).
Please verify these details, if you are still having this issue, could you please send me an email with your account info, and we can take a closer look? Please send me your email, contact info, and Company Account name you use to login to Method with. You can email me at b.citren@method.me or privately through these forums.
-Ben