If you are receiving a Magento timeout error when you are syncing your inventory, you will need to enable a setting on Magento.
The error under Support - Sync inventory history typical looks like: "Error received updating Quantity for Magento Storefront: XXX. Error: The request channel timed out while waiting for a reply after 00:00:09.969. Increase the timeout value passed to the call to Request or increase the SendTimeout value on the Binding. The time allotted to this operation may have been a portion of a longer timeout. "
This setting can be found under the Magento Admin panel at:
System -> Configuration -> Magento Core Api (this selection is on the left hand menu) -> Enable WSDL Cache