I have used Photoscore Ultimate with Sibelius 7 on the mac. Sibelius 8 is out, but I have not made the upgrade. Photoscore works well for relatively high resolution scans of print music, but once imported into Sibelius, I find you have to do quite a lot of editing to make it look good. Usually what I will do is import it into Sibelius, then copy and paste the parts I need into the appropriate staves in another Sibelius file that I created freshly. Photoscore does not work well for handwritten music, or even music in a Jazz musical typeface. Once you import music with multiple parts on a stave, Sibelius does a good job (usually) of separating the voices, then there is a simple menu command to separate them onto two new staves. This could be used to easily make a pedal part, for instance.
The past several months, however, I have been learning how to use Dorico. Dorico doesn't have a scanning and importing function, but I find that now that I have learned to use it, I can input music in multiple voices on the same stave quite quickly, probably faster even than Photoscore and Sibelius. It has a steep learning curve and a poor manual though. On the plus side, I find I don't have to do a lot of editing to make the score look good, which is a big time saver. If I was to accomplish the work you describe, this is undoubtably the way I would do it.
Another option may possibly be Finale, but I didn't like the interface and didn't spend much time with it.