Or, you could do what I do.
1. First, get the Pokemon you want, and get ready to transfer them.
2. Next, glance over the sprites to determine the colors on it very quickly.
3. Then, make the background a color not on the Pokemon, for instance, you might use a red background on Blastoise.
4. This will make sure that you don't have any transparent parts of a Pokemon.
NOTE: I use MS Paint, and use the select tool. Make sure your background (or as my friend calls it, 'right-click') color the color you're going to, well... make the background of the transfer!
Example: You used Azelf, Mesprit, and Uxie. With a glance I see no green at all, so you can make the background green. Right-click on the color that you chose in the instant-palette at the bottom. Then, use the fill tool. (And make sure you filled in those spots that weren't hit with the fill tool!) Use the selector to copy your sprites. Now, paste them into the background image you choose. Viola!