Hi,
Do you mean your webpart will be existed in MasterPage and content page, and you want to separate them? If so, I think what you can try is shaing web parts across mulitple pages by creating a custom PersonalizationProvider. So in this way, you can separate the zones in Masterpage with those in content page.
Here?s a link for you to refer which concerns on how to create this kind of custom personalization provider, maybe it?s helpful to you.
http://www.simple-talk.com/dotnet/asp.net/web-parts-in-asp.net-2.0/
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Thanks.
Sincerely,
Michael Jin.
Microsoft Online Community Support
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