I don't think that reference to System.Math is the cause of your problem, as:
(1) Math class is part of the System namespace, and as long as you have a 'using System' ref. the code can access the Math members,
(2) Your code does not call any of the methods in the Math class.
The error message that you are getting is caused by not putting the Functions routine in the same namespace that you place the MainClass (or alternatively adding a reference to the namespace where Functions is located). If you use VS and create separate classes for MainClass and Functios, then VS will automatically add the namespace references for you (I think it uses the name of the project by default). If you are creating the files using a text editor, then you need to add the namespaces yourself,