In ATG 9.1, Can someone suggest me the steps followed to maintain inventory when I go for multiple channels(Web, Store, etc.)Just giving a high level idea as there would be some customizations, integrations and other number of things involved here. ATG by default provides an inventory framework including an InventoryRepository. Part of this inventory framework is an interface called InventoryManager that contains all of the typical functions of an inventory system. Some default OOB InventoryManager implementations are provided as well. There is also a very simple admin interface for inventory management accessible from dyn/admin. I think you might be already referring to the chapter 13 for all this in the commerce programming guide:
Also how to display the remaining Inventory items count for individual store?The default inventory repository does not maintain stock levels corresponding to a particular type of channel or store. So if you want this type of functionality you can extend the default repository definition and probably InventoryManager also to account for the type of channel/store in inventory.