Sounds like you are not totally aware of how a layered architecture works.
For 3-tier architecture:
Have a UI layer
Create a class library - BusinessLogic
Create a class library - DataAccess
Now, from your UI, use the object model and pass on to BusinessLogic project class. This class is a Business logic class. Do the changes as per your need here.
Now, pass on the changed data from business logic class to dataAccess project class. In this class, use ADO.NET and pass on the needed values to Stored Procedure.
For getting back data, it will be transferred from DA to BL and then BL to UI layer.
Have a look at these, explaination with samples:
3-tier architecture in C#[
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3-Tier Architecture Examples[
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3-Tier Architecture in ASP.NET with C#[
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For uploading, you will upload file from UI only... pass it to DB using BL.