Magento order processing

Project Description:
I am in need of a some kind of application or workaround in order to process orders from online server ubuntu 10.10 running Magento 1.6.2.0 to local server running on windows server 2003, Mssql as database. We have a local network which uses this local server as a main server beside the online Ubuntu 10, MySql database. We will be working on online site as well as a local server and both are live. You need to export the new orders form Magento to the local server and match it with the costumer name and address or name and telephone no. and if available personal registration id . If not matched assign a new costumer ID.
The local server is accessed by local network to process orders and manage most of the business using a product application called FDT avance.