Your first resource for should always be the ATLAS errata file. This file keeps track of all discovered errors in ATLAS, and their workarounds or fixes. It also contains workarounds for common system problems (eg., compiler errors, non-standard commands, etc), as well containing advice necessary to get the best performance on various machines.
If you have downloaded the ATLAS source, your ATLAS/doc directory contains some useful documentation, though it is often more dated than the info in the errata and online.
If (and only if) neither of these sources provides the information you need, you can can submit a support request to:
the ATLAS support tracker.
Do not, under any circumstances, post your support request to the "bug" tracker. As documented on the tracker itself, this is for developer confirmed bugs only. All users should use the support or feature request trackers. Things that turn out to be bugs will later be escalated to the bug tracker by the confirming developer.
In addition, please understand that the tone of your support request is important, as described here.
You do not need to create SourceForge account in order to use the tracker (that persistent plea to "please log in" can be ignored), though it makes things easier if you do. In particular, if you don't log in, you won't be able to later attach extra files, etc (you can attach a file in your initial report, but afterword's, it is unsure you are the original poster, so it won't allow it). So, if you think you may need to do this kind of thing relatively often, it may be worth doing.
Note that you should upload the error_[ARCH].tgz file as well. If the error killed the ATLAS install before it successfully created the error tarfile, create it yourself by issuing the following command from your ATLAS/ subdirectory:
make error_report arch=[ARCH]
Note that the [ARCH] of the above directions should be replaced by your architecture string that ATLAS is using (eg., Linux_P4SSE1 or SunOS_SunUS4, etc).