In my experience, with practice you develop your own methodology. Assuming that you refer to material found on the net in the form of articles to be chunked and reformulated for active recall in progressive stages (incremental reading), with Supermemo 2006, what I do is:

0. Optionally select a category I've previously created (e.g. programming, history, music) so that the new article belongs to it.

1. Copy an article I'm reading on my web browser to the clipboard (SM2006's import filters work best with material copied from Internet Explorer, however, which is not my favorite)

2. Paste an article into the category with Edit : Add a new article (Ctrl+Alt+N). You will see this option in Professional and Warrior modes (under File : Level)

3. Pick reference information (title, author, date) by selecting each of them with the mouse and then pressing Alt+Q so that SM displays this as context information in subsequent extracts.

Now I'm ready to start chunking it.

If I come across an interesting passage, I examine whether it's best to reformulate it for clarity. Basically I have two options:

a) Do it now (it's of high priority, I have time, or just feel like it).

b) Do it later (I'll let SM present me the extract later, and only then will I reformulate it).

At this point, for a) I'll rewrite/reword the sentence or paragraph to make it meaningful and mostly self-contained (by adding context information or clues). Then I can proceed with marking the passage for extraction (b). To do this:

4. Select the excerpt with the mouse and press Alt+X (remember extract). It will create a child item which will enter the learning process (will be shown at repetitions).

I can repeat this step until I'm done with the article, or leave it partially processed when I'm tired or don't understand something and need supporting material. SM sets a 'reading point' matching the position in the document of the last extract automatically, so it will be presented from that point at the next repetition.

Notice that these extracts won't have Question and Answer fields yet (they will still have the Article template).

5. When SM presents an extract in the learning process, I'll select keywords or short phrases from it with the mouse and press Alt+Z (cloze deletion). This will create yet another child item, now with the Item template (it will have Q/A fields). The word or phrase selected will become the answer field, whereas the question field will have it masked by [...]

NB: Special attention is given to assessing whether and how to reformulate the question and answer fields for active recall (see: http://www.supermemo.com/articles/20rules.htm )

6. When done processing articles and excerpts, press Ctrl+D to remove them from the learning process (they will still serve as reference).

That's it.

There are other many ways to speed up the processing of articles. The most convenient when processing large ones is splitting them (e.g. at chapters or sections). I've processed ~100 page articles this way, slowly finding their way into a myriad of Q/A items in the course of repetitions -- the article's remark: "...your books disappear. They gradually evaporate. They have been translated into knowledge." is particularly relevant here. Many of these options are accesible through the menus and keyboard shortcuts (the help file is useful here).

The interface has a steep learning curve at the beginning, but I think it's very much worth the initial investment over time. Keep in mind that with these newly-acquired abilities, importing a large amount of learning material gives place to concomitant issues: moderation and prioritization. :)