I have used your method for mixing the flavour concentrates, do I add these to the base at the total % of the complete recipe (a bit confusing to discribe) to match how the recipe was intended
Yes! Exactly!
You probably can stop reading here; my rambling below just explains why this will work well for you.
The pipettes I use are 20 drops per 1ml and I don't know if its the same in the US but here in the UK FlavourArt and FAP have dropper bottles that also drop 20 per 1ml.
Those are also easy to work with, a good round number. And now I understand your complaint about the calculator! A single drop of flavoring per 5 ml, assuming 20 drops/ml, is 1%. You CAN'T make a 5ml recipe with ingredients under 1% with those droppers. You'd need to make a 10ml batch -- because 1 drop of flavoring in there (with 20 drops/ml) would be 0.5%. And you'd need to make a 20ml batch in order for a single drop of flavoring to be 0.25%. That's a lot to vape, if you don't like it!
So to avoid the need to make a giant batch...do it just like you said you are. Mix the flavor concentrates, then add them to your base at the total % of flavoring in the recipe. You'll be vaping it just as it was designed, and you'll never have to make huge batches. Even better - if any recipe is just too weak or too strong for you, you don't have to remix all those flavorings from scratch.
Does that answer all your questions? If I made it more confusing, don't be afraid to say so!