Baroque (and all Common Practice Period) composers didn't think of composing in scales; they thought of composing in keys. In minor keys, the sixth and seventh steps are mutable. (Parenthetically, the mutability of B into Bb predates Guido's writings.)
The interaction between the upper and lower forms isn't fixed; the "rules" were often broken for various reasons (that is, the composer thought the music would sound better.) There are a few practices that were used more often than others.
Roughly speaking, for a given key, harmonies are basically tonic, dominant, and sub-dominant (major and minor). If the underlying (local) harmony is sub-dominant, the lower forms of both step 6 and 7 was the most common procedure. If the underlying harmony was dominant, the raised forms of 6 and 7 were used.
If the underlying harmony was tonic, the raised forms of 6 and 7 were used in ascending scale passages; the lower forms were used in descending scale passages. (This could even cause cross-relations if there were an ascending scale passage in the soprano and a descending passage in the bass.)
A common exception was to use the lower form of step 6 and the upper form of step 7 in the melody; this was more common in instrumental music than in vocal. It was thought that the augmented second was relatively hard to sing. In later times (Haydn, Mozart, Beethoven, Schuman, etc.) this latter form was used for vocal music too.
Another few procedures of the mutable steps were often used. The lower form of step 6 was never used as a neighbor tone to step 5. The upper form of 6 and the lower form of 7 were rare (I haven't seen it.) as this would sound like a short modulation into the key a whole tone below the tonic.
The augmented chord on step 3 wasn't common until the late Romantic era.
The major sub-dominant could be used for color (using the raised form of 6). The chord on step 2 seems to occur in several ways (these are also used in major keys). The usual is as a diminished chord. The ii065-V7-i was very common (at least for the last 500 years). This easily changes to ii-V-i or II7-V-i and variations. I've sometimes used ii-V-i at the end of a phrase then ii065-V-i in the corresponding place at the end (to help the audience know when the piece ends.)
Just for completeness, the ending i chord is often changed to major (called the Picardy Third.)
Sometimes the description of the seventh step being raised to form a major dominant then the sixth step raised to avoid an augmented second is used to explain the minor mode stuff. It's a bit more complicated but still not too bad. The main point is that until the jazz-pop-modern era, keys were the basis of harmony and long-range relations between keys were a compositional tool to bind long pieces together.
