Unfortunately, it is not entirely straightfoward.
If you create a manifest file for each application, some will not work for a number of reasons (protected files, some shortcut formats not supported for colouring, certain command line syntaxes that don't work, etc). Selecting a color can be fiddly even for
one tile, as the shade only has to be out by a little to be seen as a clash with either the icon or a neighbouring tile.
I've spent quite a bit of time sorting out these problems and can now change the background of all my Desktop application tiles individually or in bulk with batch files, but color selection is too painful to do more than specify a few applications and set
the rest to a single color (or leave as is). In practice, it is still a major improvement.
Having figured out all the requirements and "gotchas", I was planning on building a small .NET app that did the same job as the batch files, but with a smart interface for bulk and individual configuration (or any combination), which requires no hooks into
the OS and makes fully reversable changes taking into account the tweaks to be made for all the special cases.
I am hoping to have it in the Windows Store in a week or three. It will be likely free, voluntary donation-ware or a couple of dollars per user (still considering the options). There are enough planned features to stage three releases with refinements.
In the meantime, I would suggest you limit fixes to addressing the odd application where the tile color masks the icon or is unbearable, as an effortless-to-apply solution is not very far away.
I would have had it done by now, but I wanted to see what changes came about for 8.1 GA, and get my workstation rebuilt with 8.1 and VS2013 before starting anything new. Prototype in batch file exists now, has been tested for a few weeks and works very well
with absolutely pleasing results. Coding in .NET is underway this week. I will post on Twitter and PinkAxolotl.com when it is ready. Should I fail in this task for unforeseen reasons, I will release the batch files and people can edit them to their liking.