SAURAV,
Are you two queries independent of each other?
(rebate and no link with group condition types?)
The reason for asking this is that in rebate condition types (BO01 etc.) there is no Group condition functionlities (as present in K029 etc.).
Thus probably you can not use Group functionality for rebate condition types.
For any discount that your company does not want to give immediately, that has to be taken in rebate. So in your case too, you might use rebate.
Where do I assign the condition types BO01 and BO02 in the Pricing procedure for factory sales(EXCISABLE).
Important is the "base value" on which rebate is calculated.
In the pricing procedure, field From specifies what shall be the base value.
This "base value" is prices + discounts i.e. value of goods (it does not include freight, tax etc.)
Thus your taxes should come after rebate condition types. Note that the values of the condition types coming after rebate condition types wont be affect by these cond types as rebate cond types are statistical 
in the billing document.