windows 98 includes an ms dos and i have heard that people have successfully run windows 3.11 simply by exiting windows 98 to MS DOS and starting windows 3.11 although i have never done this myself. I would suggest that you install the windows 3.11 on a separate fat16 partition, but probably put windows 98 on there first. the reason is, windows 98 will use a fat32 filesystem, but it can read fat16. This means windows 98 will be able to see the win3.11 partition, but not vice versa, and with these old versions of windows they really want to think they are on the first drive, so if you have windows 98 on the first partition, then windows 3.11 on the second one, both will think they are on the first partition (if you get me)
next, you will have problems installing freedos and windows 3.11 onto different partitions, because both will see the other's partitions. also remember that fat16 becomes more inefficient for storing files, the larger the filesystem is, so above a couple of hundred MB there's not a lot of point, hence your FreeDOS (if it is fat16) and win3.11 partitions shouldn't go above that size. My advice for installing windows 3.11 is this: install msdos first, then install windows, then install DR-DOS into the same DOX folder that you put MSDOS into, over the top of it. There are several reasons for this: first DR-DOS is better and has more utilities (and the same ones are better than their MS equivalents in my opinion), including ones written for windows. the windows ones will only get installed if windows is detected by the DR-DOS installer, however you need a DOS on there in the first place to install windows with.
all that's from memory and may be a couple of years out of data, but since it deals with ten year old software this might not be too much of a problem, but anybody feel free to correct me on this.