Hello, you have quite a few parts to your question here, so I'll try to give my views on some of them.
The first thing that comes to mind is that first you should find out what already exists at country level, what other NGOs are doing, and what information in collected in government health data systems.
CMAM Report (http://www.cmamreport.com/) can be used to keep data from your treatment activities. It uses standardized indicators for CMAM.
For IYCF indicators, see here: https://www.fantaproject.org/monitoring-and-evaluation/iycf-indicators
You might also think about using digital tools to collect routine monitoring or survey/research data. ODK is an open source tool that can be used (https://opendatakit.org/).
Is there any existing government database, or data system that you should work to feed your information into? Often, excel based databases are used.
There are several survey methodologies and also formative research techniques that can be used to find out more about the nutrition situation, and the drivers of malnutrition. I would first try to find out what existing information there is, either in your project area, at national level, or even in a neighboring/similar geographic area.
When you say that the prevalence of malnutrition is carried out, what is used to determine these estimates? The limitations of screening data often mean that it is not representative of the area as a whole, unless exhaustive screening or a robust sampling method is done.
For mothers screening with MUAC, there are a lot of positive experiences. Check out ALIMA's MUAC publications "Mothers Understand and Can Do it."