Leave mathematics is very simple and based on monthly and yearly basis. You have full authority to allow leave according to your wish.
No, in such case employee's leave balance will not be added and it will be eventually collapsed in the new financial year. Leave balance is only for current financial year. If you have leave balance in such circumstances salary will not be affected.
You do not need to purchase any special stationery, as most reports, including payslips, can be printed on plain A4 papers.
Obliviously you have facility to check out salary detail of any preferred employee individually.
No. If you categorize employee in fixed salary head and such employees don't fulfill attendance requirement, no effect will be in their salary. Whatsoever you have defined salary for them you need to pay. In brief, whether employ's attendance is complete or incomplete their salary will not be affected in such case.