The Designer files are pretty simple code; the only thing that you'll typically find in there to complicate matters (but only slightly) is BeginInit/EndInit calls at the top and bottom of the file--between those the code is pretty forgiving.
*That said, do not put any code in there that will only execute at Runtime. Any runtime-dependant code will fail at design-time, so trying to open your control in Design view will blow chunks. It used to give you the Red Screen of Darn, but I'm not sure what effect the IDE has notwadays--but if things blow up and the usual tricks fail to remedy them then try removing your customized sections.
Further on that note (not to scare you, but rather to hopefully head off some of the difficulties we had) the means of determining if your code is executing in Runtime or Designtime often fail if your code is not part of the currently built solution/project.
So to bring it all home, simple UI layout/winforms modifications are perfectly fine to do by hand in the designer code. Databinding and external dependencies (with the exception of calling third party control libraries) should be cautiously approached.