Let me preface this with the fact that I'm the creator of the SE proposal.
There's no reason why SO, this site, and SE can't all coexist. So far, the majority of the questions on Stack Overflow and here are related to the construction phase of the software development life cycle. And you can tell that there's isolation in the people based on the percentage committed to the other proposal. Less than 10% of the people involved in the Programmers private beta committed to the Software Engineering Stack Exchange and around 8% of the SE committers committed here. That's honestly a pretty small number.
The SE stack exchange is designed for requirements engineering, design and architecture, testing (excluding the implementation of test cases - that's Stack Overflow's territory), and maintenance practices. SE also covers topics such as configuration management processes (not tools, as that falls into Stack Overflow's domain), business and engineering management, development processes, tools (although construction tools such as text editors and IDEs are covered on Stack Overflow), software quality, and professional ethics. High level questions on computer engineering, theoretical computer science, mathematics, usability, and systems engineering would also be on topic on SE, while more specific questions would be directed to the appropriate Stack Exchange (if one exists).
Honestly, it's likely that this site, SO, and SE will have overlap in topics, but I think the target audience is going to be different. SE is specifically focused on people pursuing a software engineering degree, have a title similar to "software engineer" at work, or perform academic research into the field of software engineering. On the other hand, this site and SO cater to people who work as developers and programmers (which software engineers do...about 20% of the time).
I think that how this should go down is that SE enters private beta, we get a bunch of good questions going in the first week. Then, once SE enters private beta, there's a discussion started on the three relevant metas - SO, here, and SE - to further define how each site can "play nice" with the other two.
Right now (as awesome as this site is), its future is still undecided for another 2.5 months and the SE exchange hasn't even opened. So let's take this one day at a time, work together to build strong communities, and see what happens.