Jewish translations make no distinction between the two verses.
Rashi looks at the Amos 3:6 in context with the verses before and after 3:6, pointing out that the roar of the lion, mentioned in verses 4 and 8, is the warning from the prophets. The prophets would prophesize a threat of evil -- i.e. Divine Retribution -- unless there is repentence. So, when the evil actually comes that the prophets foretold, should anyone assume that it came from anyone but G-d?
In that context, Amos 9:4 also makes sense. The evil that comes to those who do not follow the will of G-d, is from G-d and no one else.
These conclusions are consistent with Deut. 30:15-20 where the Hebrews are told that G-d has given them the choice of "life and good" and "death and evil." The former election is assured if the person loves G-d, walks in His ways, and keeps His commandments, statutes and ordinances. However, the person who goes after other gods has chosen death and evil. This may also be read with Isaiah 45:7 wherein G-d states: "I form the light ["for the righteous" according to Rashi] and create darkness; I make peace and create evil; I am the Lord that does all these things." The word for evil in Deuteronomy and Isaiah is the same word and the same intent as in both verses of Amos.
I realize that some Christians are uncomfortable with the concept that G-d, who is all Good, creates "evil." But the creation of evil, if you will, was a necessary evil in order to make Free Will possible. G-d is glorified when his children make correct choices of their own free will, and without free will their choices would mean nothing.