Hi Elias,
When using the variable aperture mode, AIJ puts the actual aperture size
used in each image in the "Source_Radius" column in the measurements
table. All of the measurement table data columns are described in the
last appendix of the AIJ paper on arXiv here
http://arxiv.org/abs/1601.02622.
By the way, AIJ automatically calculates photometric error, as described
in the AIJ paper. This includes all sources of error, except noise from
atmospheric seeing, which can be difficult to accurately estimate in
differential photometry.
Karen