Effective & Ineffective Doctrine refer to skirmishing doctrine. They are mentioned briefly in the Artillery & Skirmishing Phase section (5) and on the corresponding chart. Effective Doctrine refers to Formations which have an effective skirmishing doctrine while Ineffective Doctrine refers to Formations which would typically be considered poor or ineffective in a skirmishing competition.

In general that would be France, Great Britain, Russia in the Mid & Late War, Prussia in the Late War, and Austrian Avante Garde in the Mid & Late War. You can find out more about it in Raising an Army (one of the supplements included in The Complete Player's Guide).

Essentially it is just a question of how good they were at employing skirmishers.

Played an 1809 scenario last night & we used the Bavarian corps. We rated them as effective skirmish doctrine because we could not find their skirmish rating in the book (& by 1809 they had adopted French battalion organization). Next week we plan to use the Saxon IX corps & French IV corps (which has a Baden brigade & a Hesse-Darmstadt brigade). What are the skirmish ratings for these 3 contingents in particular & all Confederation of the Rhine troops in general? Also if we're just being stupid & not looking in the right place, please let me know. 

Posted by: @scottzimmerleecomcast-net

What are the skirmish ratings for these 3 contingents in particular & all Confederation of the Rhine troops in general?

All of the Franco-German allies should be considered Effective Doctrine, you are correct.