My friend has an iPad and she synced one folder first, then she tried to sync the second folder, it overwrites the original folder. it means you will have to keep all your photos in one folder when you sync them it will overwrite the original one, which is ok because your new folder has the old pictures and new pictures. Ideally, every time you sync a folder, your iPhone or iPad should create separate albums for you so you can browse the photos that you want, instead of every single photos, unfortunately, with PC the iTunes can't do that, but with Mac, it is not a problem.
She even went to Apple store to see if she has done something wrong, the sales there told her that she will need to purchase a mac computer to resolve this problem. She told me that she refuses to purchase a mac to support her iPad.