Flexibility is key for extracting the most information out of a dose-sensitive cryo-sample. We show how our open-source system SavvyScan can be used to handle custom scanning patterns and support multi-channel simultaneous acquisition. Tomography and single particle analysis require quite a different scanning pattern to achieve efficient sampling. Post-processing of the multiple detector signals can either remove aberration artifacts, support compositional analysis, or achieve topographic-like depth mapping of the sample in a single scan. For tomography, our software ClusterAlign is used to align tilt series of especially thick samples, based on tracking clusters of fiducials instead of a single fiducial marker. These tools are designed to have interfaces with common software and yet offer flexibility based on a collection of custom written Matlab scripts for complementary tasks.