Hi Abdul,
if the practice is to have a separate pricing at SO level, no need to have a different pricing procedure, play with a manual condition type in both SO & quotation using the same procedure, if you want a separate pricing procedure you can go with it, but single procedure is an easy approach.
for point 2, the simple solution will be to change the account assignment group AAG, at the header level of the invoice to the one which is normally not used at all or the one where you dont have an entry in VKOA & change it to the originally available after all your manual activity. this will be for case to case basis & if you are ok to do this manual activity of changing AAG every time.
if this is required for all the documents & if such postings happen with a dedicated billing document type then go for a suitable option in billing document type level in VOFA.