In such settings I would do stages 1 and 2 of SQUEAC. This will give you a lot of information regarding barriers to coverage, treatment seeking behaviours, program performance, program outreach, &c. (stage 1) and identify issues with spatial coverage (stage 2). You can then decide whether a stage 3 survey is needed (it usually isn't but people like to do them anyway). Cases can be hard to find if prevalence is low but before deciding this you should be aware that wasting is often a "hidden problem". Data from prevalence surveys may underestimate prevalence due to hiding of sick children and because the PPS sample tends to exclude children in smaller communities (where the SAM cases may be). You'll get a good idea of how hard it will be to find cases during stage 2 of SQUEAC. It is common to do coverage surveys (like CSAS, SLEAC, or stage 3 SQUEAC) during "lean seasons" to make it easier to find cases. SQUEAC stages 1 and 2 do not need large sample sizes and can be done and yiled useful information when prevalence is very low.