Finally,  the efforts put in the Frequency Counter paid off . I tested the working of both the FC and EPICS channels that I created by displaying the beat note on MEDM screens. EricQ helped me locking the X arm ( Y arm free) thus acquiring only the X arm beat note from the frequency counter. We plotted the beat note on MEDM and clearly could see a stable beat note when the arm was locked. Now it can be said that the FC(two of course) can replace the spectrum analyzer outside and also get the beat-note frequencies  into EPICS channels. The channel names of these two beat note frequencies are:

X Arm:          C1:ALS-XBEAT_FREQ_MHZ

Y Arm:          C1:ALS-YBEAT_FREQ_MHZ

(Note: There are many problems in alignment of the arms and we could have beat note only for some time after putting a lot of effort).