- How do you measure the redshift individually?
Do you mean "individually" for each star? (Or, for more distant object, for each galaxy?) If so then you do it by using a telescope to focus the light from that star, and that star only, onto a spectroscopic instrument such as diffraction grating (well actually they are a bit cleverer than that and deal with many stars at once by using CCD array detectors, but this is the principle).
- Doesn't the movement of the galaxy relative to us cause an initial Doppler effect, adding an initial redshift in the light it emits?
Yes. Exactly right.
- How do you isolate what space does to the light from the total change?
Two answers here. On the deeper level, the answer is you do not. Redshift is neither a purely velocity effect nor a purely spatial effect but a spacetime effect. But in practice we take note of a striking property of the universe: its uniformity on the largest scales. This means that the average behaviour, after averaging over groups of galaxies, is the same no matter where you look. So we divide the redshift from any given source into the part that agrees with the local average, and the part that stands out from the average. The first part describes cosmological expansion; the second part describes what are called "peculiar velocities" which refers to the difference form the average.
- And since the only way we can observe the object is with the redshift included, i.e. since we can't directly observe its original 'color', what do you compare the observed light to when calculating the redshift?
There are details, but the basic idea is that various properties of the source give strong hints as to what sort of source it is. For example, for stars one can find sets of absorption lines. These come in recognisable patterns reflecting the atomic elements in the outer layers of the star. In a musical analogy, it is like recognizing the different sound of a violin from a clarinet. Similar, one group of lines says "I am iron", another says "I am helium". But the groups are shifted away, as a group, from their values on Earth, all by the same frequency ratio. So we have a very strong evidence that the effect is a redshift. For observations of other things such as galaxies and supernovae there are other clues in the received spectrum.