'fnkycoldmedina' has it right, first set up the antenna without the tuner, for where you will be using it the most. That can change over time, so don't put away that ladder permanently!
The 'original' instructions were basically the right way to do it, adjust the inductor for the loudest noise, then the two capacitors for 'loudness' too (on the 'S' meter). That gives you a 'ball-park' starting point. Then at low power, adjust for maximum output on a watt meter, or lowest reading on an SWR meter. It will become easier the more you become familiar with things. The settings given in the manual are only very 'approximate', what you might see if you've got an antenna system that's fairly 'close' to right to start with, and shouldn't be thought of as the settings you will end up with. They make a fair starting point though.
Since you are using an antenna that's 'adjustable', has it's own impedance matching device built into it, by using another tuner to 'move' that antenna off of it's resonant point to another means that the tuner is going to have to compensate for the antenna's built-in 'tuner'. That's going to make for some interesting results sometimes. In particular circumstances, the two 'tuners' will combine and result in a really 'nice' result. In other circumstances/instances, it'll probably be impossible to get that antenna system to tune where you want it to go. You win some and lose some, you know?
Using two or more impedance matching devices isn't exactly the 'best' idea in the world. The odds of them 'playing well' together just isn't very likely, one trying to compensate for the other get's very aggravating.
The more you 'fiddle' with it the more accustomed you get to twiddling knobs, and seeing what happens. A very good idea is to keep notes of the various settings that result in a 'good' results! There are various ways of keeping those notes, use the one easiest for you. [How about marking the tuner's settings on it's face, or in a list, or cutting a slot in an index card that'll fit over a knob's shaft and slide that card behind the knob, lots of ways. The numbers around the dials don't relate to any particular values, they are 'logging' scales. It's a pretty good idea to take the 'lid' off and see where the minimum/maximums are for each capacitor and inductor, which end of that scale is the most and least. One reason for that is that you want to use the least amount of inductance/coil as is required.
You'll also find that there will be more than one place where you can get a 'good' match with things. If you compare those 'places'/settings, you'll see that there is one of them that's just a bit 'better' than the rest. That's the one you want to use! The differences won't necessarily be 'huge', but there will be a difference.
If there are differences in those 'good' settings from time to time, it means that there's a change in the antenna system. That's a nice 'tip-off' about changes, so keep it in mind.
There are a lot of things that tuner can tell you, you'll pick them up over time.
Have fun!
- 'Doc