The system calculated dates are based on the start date or end date of the parent (depending on whether scheduling is As Soon as Possible or As Late as Possible) and dependencies. The best practices is not to set any dates manually and to let the duration field and dependencies do all of the work. Any date you set manually will override the system calculated date and prevent the dependencies from scheduling the project. There are many intricacies here, so I would recommend hopping on a Q&A webinar (http://webinars.clarizen.com) to thoroughly go over your scenarios with scheduling.
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