Signposts and Journeys are a bit like apples and oranges. Signposts are more structurally oriented, while Journeys are more oriented on story dynamics. Signposts focus on content/subject matter; Journeys focus on experiences and transitions. From a COMPLETELY analytical point of view (God's eye view or Author view), each of the four signposts appear to consume the entire "plot" of the story which leaves the journeys to be viewed as "turning points." Conversely, from a COMPLETELY experiential point of view (Audience view), the three Journeys appear to consume the entire "plot" of the story which leaves the signposts to be viewed as, well, signposts that mark progress along the story journey.
The differing interpretations presented by the two approaches is the cause of confusion between the 3 Act and 4 Act methods of understanding stories. The reality is that we, as authors and audiences of our own works, alternate between both views. This alternation has its advantages and disadvantages. The principle advantage is that we can see both the logic and feeling of the story, predict the events and understand the meaning. The disadvantage is the confusion that is created when we get the two mixed up either as author or audience.
Theme tends to be associated with "meaning" more than "prediction." Therefore, the six thematic comparisons are best worked into the journeys (on average 2 per journey). OR, if you prefer the more structural signpost approach, you can weave 3 thematic comparisons for each HALF (2 signposts) of the story. The bottom line is that material for each signpost and journey and thematic comparison (and everything else in the storyform) need to be woven together in the finished product.
We created the Signpost/Journey methodology in Dramatica to accommodate both techniques so that ALL the bases were covered. Authors will naturally emphasize one over the other.
REGARDING QUESTION #2:
The answer is that you can accomplish the comparison both ways, either by direct comparison or by juxtaposition. That is COMPLETELY a matter of personal preference and is done during the storyweaving process. What Dramatica is trying to say is that a comparison should be made between these two perspectives and the context within which each is to be shown. How you accomplish this is truly up to you as author.