Is there a way to configure burpsuite's upstream proxy direct the traffic to the local box's proxy configuration? Additionally is there a way to exclude urls from being directed to the upstream proxy.

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Upstream proxies can be configured in "User options" -> "Connections".

Burp Suite Upstream Proxy Settings

Excluding URL's works a bit different. You basically tell the upstream proxy what URL's you want to go through that proxy or you enter a URL without an upstream proxy (leave blank)

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