As you had already indicated you ought to have a system which has a solid inventory management and a sophisticated order tracking.
i know about one such system,which completely fulfills all your requirements,it is called counterpoint pos. I am quoting the relevant feature you would be interested in from it's website:
"
Order Management fulfills the needs of retailers who process orders from a website, mail order, or customer special orders. CounterPoint's Business Software capabilities include order entry, recording shipping information for shipping manifest integration, and order fulfillment of individual orders and batch order processing.
"
for more details visit the website,
http://www.counterpointpos.com