1) One thing must be clearly noted that Alimony is a final and full amount for the rest of the future of the wife. Now the rest future starts when you pay the Alimony and all the period before that for which you have paid maintenance will not be considered in it. However once you pay the Alimony as a single payment for all her future expenses there is no need of paying her any further maintenance. So already paid amount as maintenance will not be included in the amount of Alinomy since the payment of it.
2) Yes, once a maintenance is granted under sec 24 and paid it will certainly be counted while deciding Domestic violance case however two different maintenance for a same period can not be claimed through two different cases. however if the one court decided a higher mainenance the option is with the complainant to which she claims as both the cases can go along with the each other under DV Act Sec 12, Sec 24 HMA, and 125 CrPC.(These all different Acts cover Maintenance to wife).
However to avoid any discripency now a days courts keep an eye on the same relief matters and usually they club it with one if the nature is civil or criminal.