2D materials exhibit tunable interlayer interactions due to weak van der Waals bonding, which influences magnetic ordering in 2D magnets. The stacking sequence and internal chemistry impact ferromagnetic (FM) or antiferromagnetic (AFM) ordering, as seen in materials like CrBr3, CrI3, and Fe5GeTe2, where doping with Co raises the Curie temperature and alters magnetic phases. Chemical disorder also affects magnetic properties, with Mn/Sb substitution promoting FM ordering in Mn(Bi,Sb)2Te4. However, understanding how the atomic structure affects macroscopic magnetic properties remains limited due to the coexistence of metastable configurations. Precise control over stacking and chemical order is needed to harness 2D materials' magnetic and quantum properties. Transmission electron microscopy (TEM), especially aberration-corrected STEM, is today one of the most powerful techniques, enabling atomic-scale imaging and spectroscopy, for studying structural and chemical properties of 2D materials. This PhD project aims to study the relationship between atomic structure, chemistry, and magnetic properties in epitaxial 2D layers like (Fe,Co)5GeTe2, combining growth via molecular beam epitaxy (MBE) with STEM-based structural and chemical analysis.