As said, I don't think there is a best way as such. But some organisation does help you the programmer.
How often in a long project have you spent time going up and down one or more source files trying to find one of your functions.
So I make use of the #region a lot to in this sort of way -
- region Events : All of the event references that this class uses (at least in this particular partial class). 
- region Controls : All functions that directly interact with controls on a form. 
- region MDI : set the mdi up - Then there will be some to do with functionality rather than interface, 
- region Regex searches 
I sort of make it up as I go along, but using the same pattern I always use. I must say I have been told by some programmers picking up my work that it is easy to follow and others that its messy.
You can please half the people half the time and the other half a quarter of the time and the other quarter of the time you confuse everyone including yourself. I think Winston Chrchil said that.