In your ApplicationModule.js you can modify the home page collection definition of lists displayed (The main navigation buttons).  You can either add new lists that you have created or simply change the order of the lists that are shown by default.

Here is the code using the dojo.extend method of the Application itself.

            var originalDefViews = Mobile.SalesLogix.Application.prototype.getDefaultViews;

             dojo.extend(Mobile.SalesLogix.Application, {
                getDefaultViews: function() {
                    //Get view array from original function, or default to empty array
                    var views = []; //originalDefViews.apply(this, arguments) || [];
                    //Add views
                    views = views.concat(['account_list']);
                    views = views.concat(['contact_list']);
                    views = views.concat(['lead_list']);
                    views = views.concat(['custom_list']);
                    views = views.concat(['another_custom_list']);
                    views = views.concat(['ticket_list']);
                    views = views.concat(['calendar_daylist']);
                    views = views.concat(['history_list']);

                    return views;
                }
            });

You will notice the line of code where I have declared the views array.  I commented out the typical line that gets the default set of views (the OOTB list of views and there order that is defined in the standard applicaiton.js module)

Instead of returning the default list of views in my array I initialize an empty one and then I just add in the views I want in the order I want them.  The users still have access to the other views via the config section of the mobile client but this way you can control the order of the views on the home page