Apple kindly provides an upgrade path from the Macintosh SE to the Mac SE/30, which uses the same case. However, as people on Usenet have recently discovered, the upgrade is not as straightforward as one might hope. We at TidBITS discovered this the hard way recently as well and were forced to give up one of our floppy drives.
The SE comes in two basic configurations, two floppy drives or one floppy and a hard drive. The SE/30, in contrast, only has one internal floppy connector and only one hole in the front bezel, which is also replaced in the upgrade. So even though there is internal space for a second floppy, the space can only be used for a 3.5" hard drive. So if you had two floppy drives in your SE, only one of them can be retained when you upgrade. Of course, this difficulty only comes up if you elect not to upgrade to a SuperDrive along with the new motherboard. Just ask your dealer to make sure to return your spare drive and look for someone with a single drive Mac II/IIx/IIfx who wants another floppy drive.
Memory poses another problem. Dealers have to return an SE motherboard with exactly one meg of RAM on it, so if you have upgraded your memory, make sure to give the dealer your old 256K SIMMs, or if you have 2.5 megabytes of memory, make sure they know to move your one meg SIMMs to the SE/30. One person had four megabytes in his machine and expected to end up with five after the upgrade (as per a salesperson's explanation), but found that the dealer had taken the four 256K SIMMs from the SE/30 motherboard to return to Apple. A call to the dealer and the return of the original four SE SIMMs alleviated the problem.