In my opinion Paint would be easier to do simple things such as that, rather then gimp.
I am not sure what your method is for combining the two tilesets, but this is what I do.
With paint.
I simply right-click the file I want to open choose open with paint, and paint program starts with that file in it.
I then do the exact same thing to the second(or third or fourth) file I wish to add to my first.
I now have two paint windows open one with the first picture one with the second.
Normally I unmaximize both windows and stretch them to take up half the screen(vertically) My main picture(the one I add to) I put on the left side, and the second(the one I am taking things from) I put on the right.
I now have both pictures visually present both in seperate paint windows.
I then highlight the section I want from the right side picture and hit Ctrl+C(copy)
(I normally just start at the top left of the pictures pixel. What pizel you are hovering over is displayed in paint in the bottom right corner)
I would then go back to the left side picture and scroll down to the very bottom.
In paint you will see a black square in the center bottom of your picture, grab this and stretch it down, it may requrie you to scroll down a few times and stretch it again to get the length you want.
I then scroll back up so that I can see the bottom of the tileset just a bit and the rest bellow it is white.
Then hit Ctrl+V(paste) and what you highlighted from the right picture should now show up on the left.
You left-click and drag that picture to your desired spot.
Tip: It will only fit vertically exactly in spot, so if you see white on ethier side its on aligned right, or you cut a side off when highlighting by mistake.
Also simply move it down untill you see a white line between what you are copying and what is already present, then slowly move it up just untill that white line dissapears.
Since you have just placed a tileset directly bellow another tile set, all the squares should work perfectly and be aligned correctly when building.
Normally the tileset you are pasting will be longer then you can view at one time, I just paste it in sections and try to make sure that the sections I cut are at a part that can only line up one way and not be confusing.
This may seem time consuming and tedious by to be honest the whole process takes me less then a minute to have two seperate tilesets combined into one.
Tip: If you want to say combine Farm inside and Castle Town Inside into one tileset, my advice is that once they are combined graphically and you have it imported and are ready to assign it to a tileset, to simply copy the tileset that appears first vertically on your graphic. So if you took Farm inside and added Castle Town Inside to the bottom of the picture then you would copy the Farm Inside Tileset in your database to a new section and apply your bew graphic to this tileset.
The reason for this is it saves you having to configure the priority for the Farm tiles, since you copied it everything above Castle Town In will be setup perfect for Farm Town In leaving you only half the tileset to setup.
After reading this I realized it may be unclear, also I dont think I could clarify anymore.
So I took 5 minutes and wipped up a video and posted it on youtube.
I hope this helps it seems you are having problems with combining them not being easy, where as using my method I never hesitate to combine two tilesets for more choices.
http://www.youtube.com/watch?v=sJ0gnXuM0cM
Its currently processing as of the time of this post, but that shouldnt take long.
P.S. You mentioned not liking white backgrounds, if that is the case when using paint simply change the white to whatever color you want since your going to place something over top anyway. Remember there are two ways to 'select' in paint shown by two pictures, one lays the picture right over top, the other keeps "transparents"(or paints version of it, since its just white) in.
