The toilet flushes however water comes out of the one hole on each side at the base of the toilet. The toilet was clogged 1 day before... I'm guessing the clog has moved further downstream?? These 2 holes at base of (american standard ) toilet - 1 drilled on each side maybe 1/2 inch from ground - what is there purpose?

If the holes are visible when looking down, they are probably for mounting toilet to waste ring. There should be a screw coming through hole and a nut on top. There is usually a cap covering this screw and nut. If this is not the holes u are talking about, could u show us a picture?

The problem with the blockage should be able to be solved by snaking toilet.

Chuck

To clear your blockage you mast snake the line. You can either pull the toilet and snake from there or snake from the lavatory roof vent.
As for those holes, I think Chuck had the correct answer. Those holes should have bolts in them, (see image) do they? Back to you, Tom