Aik, the answer is yes and no... I'll try to explain.
Looking here, there are places for 3 base variations. Lets say you bought 3 strengths of nicotine base (24mg/ml, 36mg/ml and 100mg/ml... it was a good sale lol) and you want to use up as much of the lower strength stuff as you can because its older. That's what the nic combine is for imho. That doesn't mean you can't use it for the 24mg/ml WTA and the 10mg/ml flash as well; as long as you know the percentage of nicotine in whatever ingredient you are using IS, you can work with it.
Let me try to make this simple, hopefully. We all know that if we mix 0mg nic and 0mg nic we get a 0mg nic final result; just the same, if we mix equal parts 12mg nic and 0mg nic we will get a 6mg nic result. Anything in between is just a small calculation off of the original.
The calculator program is only doing the hard part for you, the math should still prove solid.
Getting down to it, you said: ...Need pg/vg already mixed with nic, those percentages don't change. 60/40 is 60/40 whether it's 10ml or 100mg...
I won't speak for others, but my nic base is 100mg/ml nicotine and 75%vg/25%pg. Meaning the pg/vg is already blended in to the nicotine at those levels; it's STILL TOXIC AT THIS CONCENTRATION! But, it is 75% vg. To make it into something I can use, use I dilute with pg & vg until it's about 3-6mg/ml nicotine (depending on my cravings) and then it's safe to vape, no matter the flavor as mine have no nicotine in the flavoring.
When you talk about "60/40 is 60/40", yes you are mostly right; the tiny amount of flavor (even nearly 40% flavor) will not change the pg/vg% by more than a percent or two, and unless you are allergic to pg/vg it should be almost unnoticeable.
Going on, you said "Then in the next mix, there's room to enter another nic base and that's when nic levels can be adjusted?"
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Very quickly, in terms of the formula Andria mentioned above, i used a 6% "flavor" to show me the 6% = 1.8ml of a total 30 ml batch.
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Short answer, yes. Using the Nic Combine for "unflavored" or "no flavor change wanted" will let you play with nicotine bases before tuning them with pg&vg dilutants and the flavorings you enjoy. If you had more than 3 bases (or pre-made juices) to work with, I would simply do the first 3 and keep the result for your next #1 (adding the next 2 as needed to a final result) and working from there. Blending juice can be done, but its not what ejuicemeup was intended for imho.
If I can make it more complicated, just ask lol