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I would have to reach back to advice I got from the great and recently departed Carol H. Weiss, which was if there wasn't literature on the exact topic expand to other literature where similar problems had been tackled. This proved useful advice. I don't know your problem, but I think there must be ways to find theories or practical applications from other fields where you can apply some order to your approach, even if maybe this leads to more than one way to tackle the problem.
As for the level one first or level two first, this may have to do with how you see the problem. For example, you might have a case where the top level represents institutions and you consider the variation associated with them more or less a nuisance, and you would just like to explain as much of it away as you can, so you might just add institutional characteristics in as a group or as a couple of related groups to explain as much institution-related variance as possible. Then when you explain variance using variables made up of person characteristics you it is net of the variation that is explained by observed institutional characteristics. (How level one and level two relate depends on centering of the level-one variables.) But the opposite could be true. Your study might be of institutional policies, so you might want to "explain away" the variance accounted for by individual characteristics. The thing is, for all I know, you might be looking at crop yields or something.
When I am modeling things having to do with people I tend to put variables into the model in a somewhat characteristic order by groups and test whether the entire groups significant improves model fit. Generally, I put in the demographic type characteristics of the subjects first, such as gender and age and whatever else I might have like that. Then I might have some observed psychological of lifestyle characteristics that aren't a focus of my study and/or don't change much, such as type of employment, negative affectivity, the final step is then focused on the hypothesis-related predictor(s), whatever it is I think is going to predict my outcome. But, there are many variations of this. Although the covariates are generally in the model to remove explainable variance from the error, things get tricky depending on how the variables relate to one another. So in some cases I may want to see a model with just the hypothesis variable(s) in it to understand the relationship without other variables present and see how this changes as other variables are added to the model.
So back to my main point. I think you should be as exhaustive as possible in trying to have a theoretical or at least pragmatic scheme to guide you in the process. Anything that just cycles you through a lot of tests is, according to the theories that underlying what we do, going generate findings by chance alone. That's not a very comforting thought.
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