Co-doping of SiO2 with Si and Er to achieve silica fibre amplifiers has resulted in encouraging levels of light emission, much above those of Er-only doped SiO2. However, different fabrication methods, i.e., co-implantion and sequential implantation of Er and Si, has led to several factors difference in light levels. This paper looks into the reasons for these differences by establishing structure and local stoichiometry of the created entities via analytical transmission electron microscopy. In both cases Si-nanocrystals (NCs) have formed in the SiO2 matrix. In the former case Er-ions are co-located with /integrated within the NCs, in the latter case NCs and Er are separate. By assessing the NCs' internal and interfacial structure with the surrounding material, we attempt to identify chemical/structural Er-phases/defects and their effect on the sensitising efficiency in the Er:Si-NCs system; high resolution phase contrast- and high angle dark field imaging as well as nano-scale spatially resolved electron energy core loss- and plasmon-spectroscopy carried out in an aberration corrected dedicated STEM lend valuable support to these studies.