There's a distro called Phat Linux that is supposed to specifically handle this (via a bootloader). I tried to get it running, but it's very DOS-oriented, and I don't think Windows 98 liked that very much (later versions of Windows don't like to be reminded that they're really just a glorified DOS menu system).
There's really no reason this should be neccesary, though. A dual boot is really easy to set up, thanks to the magic of LiLo. With a dual boot, you even have the windows DLL's on your system, so wine runs pretty well, and you should rarely ever even have to boot into Windows.