This is a very difficult question to answer, but I love this series, so I'll take a stab at it. I made this chart showing which manga chapters correspond to which anime episodes. It's ordered by manga chapter. At the bottom I included tables of manga-only chapters and anime-only episodes. Please let me know if you find any mistakes or oversights.
Unfortunately, establishing a correspondence between the Aria manga and anime series is very messy. For some reason, the chapters that introduced important characters were almost never adapted, and were replaced with anime-original episodes. But these episodes would often include material from the manga chapters that introduced these characters. The most egregious example is Aria: The Animation Episode 3, With That Transparent Young Girl…, which includes material from four different manga chapters and introduces two major characters, Alice and Akatsuki. In other cases, introductions very much like the manga stories were implied to have happened sometime before the series began (Woody and Al were both introduced like this.) Because of this, if you watch the anime series in manga-order and exclude the anime-original episodes entirely, you'll miss important pieces of the story.
The anime writers frequently mixed and matched scenes and bits of dialogue, added pieces of manga chapters into otherwise anime-only episodes, added substantial material to adaptations of manga chapters, merged multiple manga chapters, and partially merged parts of manga chapters. My chart probably misses at least a few major mergers (and please let me know if you find one). Many of the "wonder of the week" chapters were excluded from Aria: The Animation due to its short run, but later adapted in Aria: The Natural, which accounts for most of the jumbled continuity.
tl;dr: It's incredibly hard, maybe impossible, to watch the anime in the same order as the manga without missing parts of the story. But if you're okay with that, the chart gives you the information you need.
