It's a bit more of a hassle to learn, but I would highly recommend using the XML export/import feature.
If you use the import/export to XML feature:
You will have to re-order the trigger (T1, T2,...) and the message (M1, M2, ...) identifiers in Excel, making sure you have no duplicates. It doesn't matter that you change the T or M identifiers as along as they stay paired together.
If you want to use the copy/past method:
Create all of your triggers first. There is no copy/paste so you will need to do that manually. But you can open FTView Studio twice (two instances) one for each project. Flip back and forth as needed for the alarm trigger information.
You can multi-select the message rows from within FTView in the Alarm editor. That will paste right into an open Excel sheet. Make your changes, additions then paste back.
If you are adding more rows, you will need to have a bunch of empty rows already in the Alarm Editor. I think you can just hold down the Insert key to do that.