Eukaryotic cell membranes are equipped with special proteins that actively translocate lipids from one leaflet to the other and thereby help generate membrane lipid asymmetry. Several relevant physiological processes depend on trans-bilayer phospholipid asymmetry, including vesiculation in the secretory and endocytic pathways. The inward-oriented translocation of phospholipids is catalyzed by proteins called P4-ATPases or flippases, which belong to a subfamily of P-type ATPases. P4-ATPases, together with their CDC50 β-subunits, are essential for eukaryotic life but the key features of their activity and regulation remain to be elucidated. Therefore, these studies focus on the role of the catalytic and CDC50 β-subunit in the phospholipid translocation and the regulation processes behind it. Recent studies suggested that P4-ATPase complex functionality is highly dependent on the conformation of the CDC50 ectodomain. The ectodomain conformation relies on post-translational modifications, such as N-glycosylation and disulfide bonds. In this work, we have identified the main structural features in the CDC50 ectodomain that are essential for the functionality of a plant P4-ATPase complex. Specifically, N-linked glycosylation is essential for trafficking of the complex while disulfide bond formation is neither essential for complex trafficking nor for flippase activity. Additionally, we suggest that the role of post-translational modifications varies between lower and higher eukaryotes. The functionality on the P4-ATPase complex is essential for several cellular processes, such as vesicle-mediated transport. However, the specific role of flippase activity in vesicle biogenesis and the regulatory mechanism behind this process is still poorly understood. In these studies, we identified autoinhibitory domains in both N- and C-terminus of the P4-ATPase catalytic subunit from yeast. They regulate flippase activity in a coordinated manner which suggests the presence of a cross-talk between both protein termini. Furthermore, characterizing P4-ATPase activity is not a trivial task as these transporters are trapped in an environment formed by their own substrate (lipids). Most lipid uptake assays use fluorescent lipid analogues in combination with flow cytometry analysis. However, flow cytometry systems are rather expensive and require extensive maintenance. Thus, we present a simple and more affordable alternative using a microscope-based cytometer. This system can simultaneously provide information on flippase activity and expression levels. Taken together, the findings described in this thesis provide new tools for P4-ATPase characterization and valuable insights into the regulation and the inner workings of the P4-ATPase heterodimeric complex.