I just fired up Win98 in MS virtual PC and both autoexec.bat and config.sys are completely null (empty) files. Win95A was not so forgiving if I remember, you would have had to use memmaker which would juggle all the high memory very successfully.
If you cannot get it going, but have Dos 6.22, (you should do, since win3.11 runs on top of it) then run memmaker directly in Dos and note the settings. Then install Win95 and edit autoexec.bat and config.sys to match.
Actually, when you speak of dual-booting, 95% people would assume you mean two separate partitions, but maybe you just installed Win95 on top of Win3.11, in which case autoexec CANNOT be common to both. Even though autoexec probably ends with a WIN command in both cases, only the WIN.com earliest in the PATH statement will fire up.
I think it possible that install of Win95 is saying it must overwrite autoexec and config.sys, which you could allow perfectly ok to do that, but bye-bye to Win3.11 except by manual means. You could boot into Win95, exit to Dos, change the path to Win3.11 windows directory and type WIN which would then run Win3.11 instead.