I am sending an email with two different links to click. I want the lead owner to be assigned a task in SFDC when a link is clicked. Do I need to set up a seperate smart campaign for each link? I want the same task for both links.
No, you can simply create one Smart Campaign with a trigger "Clicks Link in Email" - then specify the email you sent. You can use a Constraint to specify the two links that should trigger your Smart Campaign; otherwise it will trigger based on any link in the email.
In your flow, you'll have a flow step for Create Task in SFDC.
If the tasks would be different, depending on the link that was clicked, you can use an "Option" with filter "Clicked Link in Email"