As fas as I know the only way you can change what shows up on the Xbox One SkyDrive app is to make sure the folder type is not listed as "pictures" and instead listed as "documents".
However with the SkyDrive app for iOS, in order to use the camera backup feature, it automatically uploads to a 'camera upload' sub-folder in the 'pictures' folder whether you have one created or not. (It will create a new one) and so everything shows up on the Xbox One Skydrive app.
Are there future plans to have this changed? As of right now I cannot use my camera backup feature on the SkyDrive app for iOS because my Xbox is at another house and I don't want the people living there looking up all my pictures before I find the time to go in and copy/delete them.