I think it depends on how much the manga fits your list. In my case I just HAD to make a separate doujin list because my other list get too crowded or overloaded if I add all the djs I liked there. However I kept the top best ones that are extremely hot or cute or have a unique plot in the respective lists. For others I made a separate list.
This is strictly my personal opinion. Please, feel free to ignore it - You should keep the ones that perfectly & highly fit your pwp uncensored list. For others you should make a separate list. Otherwise you might have the similar problem when you are near the "200 manga" limit.
so i am about to mark the doujins that i've read in the past as read so here comes the inevitable question: shall i include it in my pwp uncencored list? http://www.mangago.me/home/mangalist/36736/ i am worried that it will muddle up my list and such but there's really some doujin i know that are really hot. will anyone be bothered if i add plenty of unoriginal mangas? i have kept it like that till now.