It really has nothing to do with the amp assign feature. The X4400H has 9 internal amp channels, so to use 11 channels for the main zone, you simply add a 2 channel amp, and use the height 2 pre-outs to drive it.
The re-assign feature is there so that if you are running 5.1 or 7.1, the unused amps can be re-assigned for other purposes such as bi-amp, zone2 and/or zone3. It gets complicated, so before you do any of those, refer to the table on page 44 of the owner's manual.
Not all the internal amp channels are re-assignable, for the models below the flag ship model, you cannot re-assign the height channels, again refer to 44 where the speaker configuration and amp assign settings are tabulated.
The AVR-X8500H is the only models (also the older flag ship models, the AVR-4520 and AVR-X7200WA) that allow you to re-assign any of the internal amp channels except the front left, center and front right channels. Even the top Marantz SR8012 does not have this feature.