Thanks for your response. That makes much more sense. Here's a follow-up. If my model of interest is a random effects model, and I want to generate missing data for NHIS survey data where the data are stratified and then clusters sampled in each strata, how can that be done? There's a hint in the first paragraph on p. 673 here:
http://www.denveremresearch.org/phocadownload/outcomes/articles/advanced_statistics_missing_data_in_clinical_researchpart_2_multiple_imputation.pdf. "...separate MI models are generated for each strata within the sample, with clustering accounted for within each stratified MI analysis." Does that mean PSU must be treated as a random effect in each stratum during the imputation or is everything a fixed effect?