Sorry - last post was from my phone
Yes, use "Save as" and save the new MSQ with a new filename, I usually use the date followed by a number if I have done more than one in a day. i.e:
03_03_2013_001.msq
03_03_2013_002.msq
03_03_2013_003.msq
That way you never lose a tune and can go back to it if you need to. I sometimes break from this convention if I have made any major changes to the tune that I want to remember.
If you were just to use the "Save msq" option it would save over the msq you just analysed- which could cause you to come a cropper if the ve analyze went fubar and cocked things up at all - happens, computers are not infallible.