It is true that the Malawi SPA 2014 was a census of all health facilities (HF), the HF weight FACWT is a non-response weight for correction of non-responses. It is better to use the weight variable in your analysis. The SPA survey is slightly different from the DHS survey. For HF survey, there is no cluster variable. But you can declare the HF ID (FACIL) as PSU variable, there is no effect. For providers and clients survey, there is a cluster effect, HF is a cluster of providers and clients. So you should declare HF as cluster. The stratification is defined by crossing region by HF type (REGION crossing FACTYPE). Urban/rural was not taken into account in survey design in SPA surveys.
Hope this is helpful.
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