I'm trying to load a private map, with layers from the iOS SKD and I found the a couple of issues.
To load the map, I'm using
[AGSWebMap webMapWithItemId:userMap.itemId credential:credential];
The map loads fine, but I have the following notes.
1) The changes that you're making to the web portal maps are not propagated to the iPad unless you press 'Save'. This makes sense, however is confusing. It is possible to make some changes to the web portal map (add/rename/remove layer), then navigate away, logout, log back in and the web map changes you made last time are still there. I had the feeling that they were saved to the map, but they seem to be in a 'work in progress' mode.
2) I've added a 'map notes' layer and named it 'Test MEL'. I've added a couple of squares on the map and saved it. On the iPad, I got 4 layers named 'Test MEL 1,2,3,4'. When I deleted the 'map notes' layer (and saved the map), the 4 map layers were removed from the iPad map. This is fine, however, I would expect to have a 1 to 1 mapping from the portal web map layers to the ipad web map layers.