Dear friend,
(1) The self-stated details of your first query are themselves indicative of its answer. All the employees including managers, supervisors, permanent employees, outsourced contract labor, casuals engaged in the manufacturing activity are "workers" under the Factories Act,1948. If the no of workers inclusive of all such categories mentioned in the factory licence taken in 1999 and renewed thereafter annually remains less than 47 as of now, you have to get it suitably amended.
(2) Any establishment is decided as a factory or otherwise depending on the predominant activity carried on therewith. If the predominant activity is manufacturing, it would be a factory as defined u/s 2(m) of the FA,1948. The definition of " manufacturing process " as given u/s 2(k) of the Act covers a variety of separable activities concerned with the manufacturing process. Hence the application of the predominant activity test. For instance, we may take an automobile show room which normally comprises of sales and service of the automobiles and their spare parts. But here the activities of sales and service can be easily separated. Therefore, the part of the premises where the workshop is located would certainly be a factory u/s 2(m). The other part comprising of the show room where sales are conducted can be a shop. But if the factory licence is taken for the entire premises, the show room area would also be a factory and the sales personnel would also be workers under the FA,1948. And it is the normal practice adopted for the sake of managerial convenience and uniformity of compliance. Take the case of a sweet-meat shop where preparation of sweets and savories and their sales is done simultaneously in the same premises, it will be a shop only and cannot be a factory just because power is used for the preparation of the sweets. Yet another example is a tailoring shop where no sales are done but the clothes of the customers are stitched and delivered to them. Here the predominant activity becomes cutting and stitching of clothes may be with or without the aid of power. It would be a factory u/s 2(m)(i) or 2(m)(ii) of the FA,1948 depending on the satisfaction of the parameter of the no of workers employed therein. That's why in some states they are notified factories u/s 85 of the FA,1948.
(3) Coming to your third query. Service conditions of employees differ according to the types of establishment. Therefore, you have to maintain only the registers, notices etc., pertaining to the Act which applies to your establishment.