The template file is not locked up in any way. Feel free to change it however you need. Changing it, does require investing the time to study the layout/table/script design so as to be successful in making the changes you want.
When importing data into the contact manager, theres a little dialog that pops up that asks if you want to enable the auto-enter options. If you don't select this option, you will have trouble with your imported records as each imported record needs a serial number to be assigned to it in order for all the scripts to work. This option should also trigger the creation timestamp field to auto enter the current date and time.
"I also need to import notes from an .xlsx file to the contacts section of this template...can this be done? "
You should be able to import this data, but if they represent notes that need to be linked to specific contact records, you'll need to figure out a way to match your data to specific contact records and that could get a bit tricky depending on exactly what you have in your file. You may need to figure out the contact ID number of each matching contact and add that to the spreadsheet prior to importing.