I think it's the coordinating editor's responsibility to decide what order he or she would like them to show up in, and set the dates appropriately. For issue 1, I did this by setting them all to the same date, and mucking with the actual hour/minute/second time to control order. The most 'recent' (ie, the latest) time will show up first.
<del>I also made a mistake with issue 1 though, thinking the date didn't really matter except for this. In fact, the date/time should be set as close to the actual publication (that is, making public) time as reasonably possible to keep feed readers from getting confused. When I had the date of the post set to a few days before the actual make-public time, this caused the code4lib planet feedreader to put the posts down at the bottom of it's screen the first time they showed up in the feed, since it was ordering by date (reversed). So coordinating editor should probably set the date/hour to be close to date of actual publication, and then mess with minutes to determine order on ToC?</del> When you publish an issue, the Issue Manager plugin will give you the option of sorting the articles it is about to publish. Move them into the order that you expect them to appear on the home page, set the date and time you want to publish, then click "PublishIssue".