MBE deservs better answer, since I'm not sure if I understood question right....
Anyways, such a little detail never stopped me.
If I understand it right, you have a DIY quadrature encoder that has two channels with 90 degree phase difference and 50% duty cycle each. Normally these outputs are marked A and B. Both produce sguare wave.
Challenge is to adjust opto/HAL/whatever couplers mechanically to a correct position to produce 90 degree phase difference?
Here, for demostration purposes I adjusted signal generator to simulate those signals CH1/CH2, same wave form, same duty cycle, 90 degrees phase difference, the real scope on background shows this.
If you connect either encoder outputs (A/B) against the ground to this one channel scope you should get nearly identical signals. Both channels in isolation should produce "perfect" square wave. Only thing is, that probably mechanics is not accurate enough to produce nearly ideal 50% duty cycle i.e. ON and OFF state signals should be of same length, but probably are not. I does not matter in the end if you use only rising OR falling edges of the signal (i.e. twice the one cahnnel resolution, not 4x), but the signal "looks a little funky".
If you connect your single channel scope between hot wires of A and B channels, you'll get interesting signal, that should allow you to adjust (mechanically?) nice symmetry for the signals. This should look like the signal on this toyscope on front on my attached picture here.
When you connect the scope input between A and B signal wires, you'll get the product of these signals and the product should look symmetrical. Since you are adding two identical signals that have a 90 degree phase shift. A little "tweak" will show very nicely on the signal and since human eye detects change easily, that sort of signal will produce pretty good adjustment accuracy.
The signals could be added with a resistor network or such and utilize the the signal form factor, but then signals should be pretty stable to start with.
Was any of this anything you asked?
I find the old school analog scope easier to use. From the panel you see all adjustments on one go and nothing is hidden in the annals of menus....Of course DSO:s normally have the magical button that will find tha signal and display it....but then I'll spend some time trying to figure what settings are those numbers on the screen.
Pekka