1) If it is a salary , you can book it as a salary under indirect expenses but though its a workers salary you should book it as a wages under direct expenses . As far as concerned about the pf & esi you should read & understand the formulas of it , how much contribution of Employer & how much of employee . If you are doing accounting of the employer side then you will have to make provision of pf & esi as per the calculations .
2) Labour Payment - wages - under Direct Expenses if it is a manufacturing company.
3) Didn't get your 3rd point but Rules may be differ from one to another .