This is a rather broad question, so I will give you the high-level steps of what needs to be done:
1) Create a Custom Object using Build; Create; Objects menu.
2) Save your enterprise WSDL under Build; Develop; API menu. Typically you open the wsdl in a browser and save the web page as something.wsdl
3) In .NET create a web service reference using the enterprise WSDL you saved in a local file
4) You can write and read from to the custom object (or any Salesforce object) using the SF API. To do so, you will need to write SOQL.
Once you have step 1,2,3 done, then you should look at the SF documentation on binding to the API and how to run insert and update statements in SOQL. It is too much info for a SO question.