For me, the key to getting through the first couple of weeks of school is organization. Even before school started, we went over supply lists and stocked the boys' backpacks. That avoided the long lines and stress of going shopping when everyone else was, after the first day. I also get the school calendars and get all the important dates – Open House nights, concerts, field trip days, etc. – into my personal calendar as soon as possible. That enables me to see conflicts way ahead of time and work around them. And after that's done, I try to get everyone into a routine. Homework is started before dinner, bedtimes are strictly observed, etc. I find all this planning makes the start of the school year a lot less stressful for all of us.
After that, I make sure to check in a lot with the boys during the first few weeks. I ask them very specific questions about their teachers, classmates and assignments to see if it sounds like any small problems or challenges might be creeping up.
And finally, I make sure I've got all the contact information I need so that I can discuss any issues that arise with their teachers or other appropriate school staff members. (You don't want to be searching for an email address when your child's having a meltdown over not being able to complete a homework assignment, right?)
There are great resources online with tips for making a smooth transition into the new school year. Here are some that I found:
American Academy of Pediatrics: http://www.parent.net/article/archive/15tips.shtml