If you lace them securely from the start, you have a chance of having them form to your foot in a manner that doesn't shift. Once they start to slide to the side, it's probably creasing that's not (easily) reversible. At that point, you could have a cobbler stitch one side of the tongue to the upper. It's pretty simple for them to match it up to a stitch line already present on the outside of the boot. Disclaimer: This is not science, but my interpretation.
http://youtu.be/3PycZtfns_U In all honesty, you just need to apply it all over, and let it absorb. A hair dryer can help with the second part, but you need to be careful. Then, remove the excess that didn't absorb and buff them like crazy, and this part can be done the next day.
I don't think you're alone in that sentiment. Now, I haven't completely cast the brand aside, as I appreciate Eric's style and the one-man nature of his operation. However, the expediency of his shipping process has caused me to reconsider ordering a few items, especially as gifts.
If it continues to concern you, you could take them to a cobbler and have him stitch one side of the tongue to the inside of the upper. It shouldn't be hard for them to line it up with stitching already present.