No, do not do that! Open the Tileset in Paint, copy and paste your new tiles over the old ones, then recolour the new tile to for the pallette! It is better than indexing, as you get control over how it is coloured.
No, that isn't the problem (In my experience, that isn't too good). Did you recolour your tiles you wanted inserting with the colours of the Tileset? (Using the Dropper Tool in Paint, the one like the things you take Eyedrops with)