1. For your query one our view is that after paying the capital gains arising from transfer of property X you can clear loan on property Y or you can do whatever with that amount. If you want to invest in capital gains account then you need to put the full amount or gain amount as per various sections of the Act.
2. You can always give standing instruction to the Banker to credit the interest accrued on Capital Gains Fixed Deposit to your savings account every year and the same you can withdraw any time. The Banker will deduct TDS on the interest amount which can be claimed at the time of filing returns
