Oh really!! Can I indulge you in some quick instruction? There are others who might find this useful!!
I'm afraid I only ever played with it, and for various reasons most of the time I only use Aladin 7 (it's a standalone 32bit .exe that launches quick, though is flakey at times and doesn't always do what it is supposed to). I do at other times use the aladin10 jar, but to me like all software, the more bells and whistles they add, the more stuff ends up less usable.
So, again, I played with it a bit once, it seems to match images with circles around them, no doubt a fixed aperture thing, but relative to the star size if I remember rightly (must be three years since I last played with it, I like to play with catalogued photometry, not measure it) and then does some simple psf (point source function, the sort of thing that takes a cross section and you get a guassian, or 'bell curve' as they like to say in usaland, and do maths on that to derive the magnitude. I assume the code gets all the other info it needs from the fits header of the image, but I don't really know how it works, I'm not into kit, it takes too long to learn and I need to keep up on my physics and TRY (somewhat unsuccessfully most of the time) to extend my maths skills.
There seems to be an option under the IMAGE menu drop down, "greyed" out when there is no image loaded. It used to be a SEXTRACTOR option, so I don't know how much it has changed. I'm still on Aladin 10 as I can't update my java any further on this particular box. I think it's aladin 11 at least now. I know it keeps nagging me to tell me a newer version is available, no matter how hard I try to turn that off! I think you just used to be able to hover the pointer over a star and the mag appeared in the dialogue bit below, where the vizier text info etc tends to crop up.
Aladin is still the best fits (image) viewer I've seen, topcat the best fits (table) viewer. Zooming and the pixel histogram get a lot of use. However, now 10 does RGB, or colour in general images, the pixel histogram has separate RGB graphs that have to be fiddled with individually, but not also a monochrome one or alternatively a way to lock the three against each other, so you can shift them all at once to the exact same spot.
Ball's back in your court : þ Aladin's made to be part way intuitive, be brave.