Shashank,
Could you think in the lines of the below suggestion -
In the pricing procedure, For the manual condition type (which is applicable only for some customers), activate fields manual, required.
And in the requirement have a routine that activates this condition type only for a list of customers.
The ABAPer while creating the routine (requirement) can either have a table in which the list of customers are maintained or can have these customers hard coded.
At transaction level, in the sales order, if it is created for one of the customers in the list; the requirement shall get fulfilled and the manual condition type shall have to be filled. Or else the sales order would not be saved.
If the customer is not one of the customers in the list, then this condition type shall not feature in the sales order, as the requirement is not fulfilled.