Hi Jason,
As Jack mentioned, PixInsight has been evolving at an exponential rate - and this strain on limited resources has meant that the 'manual' has never been written. In fact, it may never get written.
This is because a 'written' manual may never be truly useful for such a dynamic application as PI - by the time the manual was written, it would be highly likely to be obsolete
![smile :)](http://pixinsight.com/forum/Smileys/default/smile.gif)
Instead, there are the new 'official' video tutorials (authored by the P-Team) and the 'unofficial' videos authored by Harry Page. Both sets are an EXCELLENT source of information.
As is this Forum.
Honestly, no matter what your skill level might be and no matter what your experience with PI might be, your questions will be happily answered as best as possible by others here on the Forum.
As to your actual questions, the "stacking" and "combining" of images within PI is still at an early stage of development, with the hope that "calibration" of your data can also be included in the near future. Many users are currently relying on DeepSkyStacker (which is freeware) to move them past that stage, and then using PI to polish up their resultant image. Maybe you are also already using DSS?
If you let us know what equipment you are currently using, and your typical data gathering process, others here on the Forum might be able to give you a good head-start on a suitable methodical approach.
Welcome aboard, and fasten your keyboard safety belt (your life-jacket is under your seat, etc.).
Hope this helps.