Is there a way to change the syntax colouring for spelling in TexWorks?
Currently red for comments and underlined red for mispelled words doesn't really stand out.
Underlined text is hard coded by developers of TexWorks and cannot be changed.
As for the comments you can define your own rules for syntax highliting in a syntax-patterns.txt file in your TeXworks\configuration folder. After that you choose your syntax coloring from the top menu: Format -> Syntax Coloring.
This is an example of changing comments to blue. Add this to your syntax-patterns.txt file.
# comments
black/cyan;I Y %.*
Here is a reference for more information.