There is a benchtop machine forum for your Sherline questions. http://www.cnczone.com/forums/benchtop-machines/
There is nothing really specific to Eagle or best practices.
I do suggest that your Eagle has a 10x54 table with about a 13x32 work envelope. I have one just like it Is yours a 2 or 3 axis? Mine started out as a 2 axis.
Standard safe practices? Keep your fingers away from the spinny things. Know exactly where the E stop button is. Make sure you know exactly where the table is going to go when you push the GO button, and make sure the tool isn't going to smack a clamp on a move. Air cutting is your friend when testing new programs.