Dear Jayarani,
Simultaneous application of several Labor Laws to any establishment possessing the characteristics of industry is dependent upon so many factors such as its nature of activities, number of employees as a whole or unit-wise, subject-matter of the applicable Law, locale of the establishment etc. To explain it by means of examples, the Industrial Disputes Act,1947 would be applicable in matters of industrial disputes; if your Administrative or Head Office is situated in an area covered by the Shops and Establishment Act, it would be an establishment under the Act irrespective of its no. of employees; if the total no is 10 or more and 20 or more at any point of time, then the Payment of Gratuity Act,1972 and the EPF Act,1952 would be applicable respectively to the establishment as a whole including the employees of its other units; if one of its units is engaged in any manufacturing process, then that particular unit would be a factory under the Factories Act,1948 based on the number of workmen cum usage of power; if the employment in any such units are covered by the schedule of the Minimum Wages Act,1948, then such units would fall within the purview of that Act. When a charitable organization engages itself in multifarious activities through its employees with their systematic co-operation in different units, as a whole it becomes a composite organization whereas unit-wise different ones based on activity-wise. Therefore, no one can give you a comprehensive answer to your question. Better, approach the concerned authority under each Act about which you are doubtful.