The report in the RTX directory are the most recent versions, and are updated for each version update. IS Tech does not automatically change the RTMs in the EvoERP/DBSMFG directory because many of us have customized our local copies. To update to a new RTM we are supposed to copy the new version from the RTX folder and rename it to .RTM after which we can edit/customize the report as needed.
 
The Evo notes data are stored in an ugly file in the root, but are referenced by unique ID inside the company. It works and should not care if you move companies around. I have my own complaints about the method because Evo notes cannot be accessed for reports via ODBC (Crystal, Access, Excel, Web, etc.) When your data is not in the database it becomes much less useful  

You can print the notes on forms such as PO or Invoice by selecting the appropriate type when the Note Printing box pops up.

If you use CSN Note type for certain Notes (Custoemr, Vendor, Sales Order) they are also saved to the old files where they can be accessed.

Yes, since Item Notes did not exist at all in Classic, there are no CSN notes saved in the "old file" because there is no "old file"

No, you need to run SM-N-C once to get your existing Classic Notes moved to Evo CSN Notes.  After that, saving the customer, vendor, Sales Order etc. will also save the CSN Note info to the old file.