I've had success installing the game in both Wineskin and in CrossOver, with both the versions of the game available from GamersGate.com and from GOG. I'll be focusing on the GOG version (and CrossOver) for this discussion here.
Using CrossOver's Windows application installer, the game installs out of the box with no additional configuration needed. There are some minor patches available that have been released from fans, but the main patch you should be concerned with is the newly released 1.3 community patch, put out just this June by DGibson. You can find out more about it on DaikatanaNews. It offers some much-needed fixes and improvements, such as widescreen support (including 16:9 and 16:10 resolutions) and some minor AI fixes. It also gets rid of the infuriating "tick...tick...tick" noise that the game spits out at you during the loading screens.
Installation is easy; after downloading it from the link at DaikatanaNews.net (the link at DGibson's BitBucket site doesn't seem to work for me as of this writing), expand it using a utility that can open 7zip files.
Everything at the root level of this folder should go into the root level of your Daikatana install folder, except the items in the "data" and "dlls" folder. Everything in the "data" folder should go into the "data" folder of your Daikatana install. Everything in the "dlls" folder should go into the "dlls" folder of your Daikatana install. Do not do a simple replacement of one folder for the other; make sure you copy over the files from the patch into the same locations as the items they are replacing.