Hi Aarif,
You can transfer the inventory from one site to another site by going to the following window.
Inventory >> Transactions >> Transfer Entry
But you cannot transfer inventory between companies using the above. Either you can do a transaction entry to reduce the stock on one company and book another transaction entry on the 2nd company to increase the stock. If you wanted to do this with one entry then either you can use addon product which does intercompany transfer between companies.