I used Toodledo for a few years so can tell you what I did with it as my GTD system.
Are you asking about the online version or the iOS (iPhone/iPod/iPad) version, or both?
I used both but found the iOS version poorly designed and not very intuitive so I used Appigo's 'Todo' instead. It syncs very nicely with Toodledo and in my opinion has a great interface and is much more intuitive. There are also other iOS apps that sync with Toodledo.
Here are a few things I did to customise Toodledo that apply to both the online and iOS versions:
1. Turn off fields
Toodledo has too many fields. Turn off as many as you can to remove on-screen clutter and save yourself time when creating tasks. I turned off these fields:
- Start Date
- Start Time
2. Use Folders for projects
I tried using tasks as projects with sub-tasks as next actions but it's easy to miss sub-tasks depending upon how you've set up your view settings. Folders become your permanent and visible place-holder.
3. Use Tags for areas of focus and use only one tag per task
There is a temptation to use tags like you would see in blog posts (e.g. multiple tags per task). This results in a big number of tags and becomes difficult to use as any kind of filter. I just had two tags: business & personal. This gave me an easy area-of-focus switch when I needed it and also a way of sorting views.
For the online version, saved searches are very useful. You can use this page to create your own custom views for easy access.
I switched to Appigo's Todo Online last year and still use Todo on my iPhone and iPad for a few very basic reasons:
a. Todo permits manual sorting
b. Todo has an inbox
Users have been asking Toodledo for these basic features for many years but I don't think it will ever happen.