Ello. I have my main menu on the main site which has automatically had modules created for it in the mobile versions. I am going to use Iphone as an example, basically when I go to my site via my iphone I see the mobile tempalte (thats fab) but it shows me ALL the menu links when I don't want it to and I can't figure out how to disable certain links for the mobile themes.

E.g I have links called chatroom/gallery & donation these three don't look right in the mobile theme they go outside of the frames so I wont to remove them from the mobile menu so they are not visible to mobile users.

How do I do that?

Hello charlie,
That is something already implemented
Just go to the menu module of the relevant template (say, in case of PDA template, it is mod_mj_pda_menu by default). There in settings of that module, on the right pane, go into 'Other Parameters' in which you will see an item called 'Exclude Menu Items'. There, enter your comma seperated values for menu items you want to remove for that template and they will be gone!

Great! Just what I was looking for. Typed menu ID and it was gone.

This is a great option, except when I want to add menu items that are only accessible via the mobile device. In this case I create a new menu through Joomla. Then I edit the main menu and copy all items to the new Mobile Menu. Then delete items from the mobile menu that you don't want the mobile device to see... plus you can add menu links to the mobile menu that will not be accessible to the Desktop... i.e. Lets say you have a calendar on your website. You want the mobile device to be able to access it, but you don't want to try and shrink a monthly calendar view down to a mobile device screen. Using the secondary menu you can create a link to a page where instead of seeing the full month calendar, users see the agenda calendar.