I've not used the stuff from Stew-Mac directly, but I have used the Trans-tint, which is what I believe Stew-Mac carried prior to putting their name on everything (feel free to correct me if I'm wrong). The bottle and cap look identical, and the instructions are very similar. It could be the same stuff.
I've had success with just using a natural oil-based stain, which is simply stain with no pigment. Just start with a few drops, experiment, and test on scrap. Let it dry thoroughly before adding more tint, as it will look different after it dries.
And I'm not sure what you mean by "before adding the oil or after". If you're meaning mixing the tints to obtain different colors, I don't believe it makes a difference when you mix them.
I can say that depending on what product you use as a base, it can take a few hours for the tint to bond with it. I made some amber stain using some Jessup's natural stain. I tried to use it immediately, and the pigment didn't dissolve right away. I had some brown "chunks" in my test. I let it sit overnight, and had no problems the next day.
I personally avoid Minwax products. See if you can find some General Finishes or Jessup's, or other good quality stains that have been recommended here.