Hey.

To be Eligible for AIIMS you should have passed Class 12 under the 10+2 scheme/senior school certificate examination (CBSE) or Intermediate Science or an equivalent examination from a recognised Unievrsity/Board from any state with English, Physics, Chemistry and Biology as the main subject and passed each subject individually. So your passing critera should be according to the marking set by your boards only. Other than that you need a minimum aggregate of 60% if you belong to the general category in PCBE. Hence,i think  if you've completed it from a recognised board, then it should be considered. Also no, 11th marks will not be considered only your marks in 12th will be considered.