You can go either way but it doesn't hurt anything leaving them in, and if you get the plates with the dimple in them you don't even need to remove the screw on top. With the dimple plates its as easy as removing the stock cover and bolt on the new plate and your done.
There $18.50 & free S/H on this site, and the quality is top notch
http://www.vtx-parts.com/honda-vtx-fury-1300-1800-pair-valve-cover.html
There $18.50 & free S/H on this site, and the quality is top notch
http://www.vtx-parts.com/honda-vtx-fury-1300-1800-pair-valve-cover.html