Kind of odd that you say there are a lot of customizations using VStools, but you don't know the Sales Order Procesing tables. Did someone else do the customizations?
To attempt to answer your questions...a lot of tables. I agree with everyone else, you don't want to "fix" the data yourself- it's quite complex and if you don't even know the tables, then you are probably not at the level where you can interpret the GP logic by looking at the data.
If you are just trying to research what may be the issue, I would start looking at the SOP tables and the IV tables
If you have heavily customized GP, then I would assume you would at least know to go to Resource Descriptions to get the table names. After all, to use eConnect, you need to have a working knowledge of a lot of the tables themselves.
As far as all the fields, that is quite complex. Perhaps you should narrow down the scope of your inquiry. Are you saying items are not being allocated properly when a Sales Document is created/fulfilled/posted? Or, Items are not being updated when Inventory transactions are entered?
Let me stop right there..I agree with Steve...what is the actual problem? Perhaps an example might help? Like if you were to say that that when posting a Sales Doc, the Item Quantity Master or the Item Bin Master was not updated with the correct amount. Be specific, though, and quote some numbers.
Before asking how it all works, you should read the SDK's and familiarize yourself with the GP model. These are available at Customer Source.
Unfortunately, when you ask what "...tables affected and what fields affected inside these tables...", it does end up sounding like an attempt to reverse engineer GP and this is not the place to post a question like that. I hope that is not your intent.
Thanks
-Dan