Assuming the sample to be a solid and metallic/semiconductor in nature, SEM accelerating voltage (or gun voltage) and working distance are 2 crucial parameters to consider for an EDS map.
Voltage 15kV or higher is recommended for EDS quantification and mapping while keeping the working distance of 7-8mm. These should be of course adjusted as per the variation in atomic weight of different samples.
Additionally, sample morphology and quality of focusing is important. With a surface having scratches, there are chances of signal loss. Similarly, the signal would be bad with poor focusing of electron beam over the sample surface.
Further, the magnification should be decided based on the feature size. If they are better resolved at 10k X, there should be not be any issue in getting eds map.
My sample is a martensitic PH stainless steel and is mounted in conductive resin. I work mainly at voltage of 10kV and WD of 8-9,5mm. The metallographic preparation is perfect without any scratches on the samples surface, so I dont thing that it is a problem in this case.
The purpose of the eds mapping is to get a view of the distribution of Cr, Ni, Nb and Cu nanoprecipitates if possible. In 10000x magnification, I get good image of Cr, Ni and some richer areas (like clusters of Nb and Cu), but not a big difference regarding Cu in martensitic matrix and in ferrite.
if you are looking for nanoprecipitates that are embedded in the matrix which are really in nano-scale regime, it would be difficult to image them with good resolution using SEM.
Also the concentration levels would be important, if Cu is present in less amount and not distributed evenly then it might be difficult to find. However, bigger clusters as you mentioned would be identified rather easily.
You should work at that magnification that gives an efefctive sampling pixel size that is roughly equal to your spatial resolution; so you need to estimate the contributions of probe size and interaction volume to the efftective resolution. If you work at lower magnification, you potentially can loose information. If you work at higher magnification, the maps will be noisier and eitehr cover a smaller region or acquisition will be slower, but you can bin the data afterwards.