Reset the Layout on the DockManager

You can use the DockManager.CloseAllActiveToolWindows method to close out all the tool widnows, thereby removing the layout.

Ok, so basically I need to close the windows and reload as required.

Yes, that's it.

That works almost as expected, however all the items when activated resume in the positions that they were left in. I need to load them so that they are displayed in their default positions (ie when the system first loads). Am i doing something wrong?

Right the method I gave you will simply close them all but not update dock positions.

By default positions do you mean how they were in the designer or just when you programmatically create new windows?

As they are in the designer.

For that you'd have to save a separate layout file. You can even do it on your end by running the app and saving the layout and including it as a manifest resource in your assembly. Then load it whenever you need to. That will keep your original layout always available to end-users and will have the effect of loading everything like it was originally designed by you.