Timebomb: Give Tabitha Smith a power action and place up to two hindering terrain markers in non-adjacent squares, that aren't blocking terrain, within range and line of fire. At the beginning of your next turn, remove them from the game and deal 2 damage to each character occupying one of those squares and 1 damage to each other character adjacent to one or more of those squares.

Time Bombs says to place the hindering terrain squares in non-adjacent squares... non-adjacent to what?
To each other. There must always be at least 1 square between the two hindering terrain squares placed by any given Tabitha Smith. You can place the squares adjacent to Tabithat, if you wish, or you could even place squares from different Tabithas adjacent to each other, but two squares from one Tabitha can't be adjacent to each other.

If I place two squares of hindering terrain with Time Bomb under a character with a very large base (say, Fing Fang Foom). How much damage would this character take? In otherwords, can I stack damage from Time Bombs?
No, you can't stack the damage. The power description says you deal 2 damage to a cahracter "occupying one of those squares"... so whether there are one or twelve hindering terrain tokens under a character, it will always "occupy one of those squares" so it will be dealt only 2 damage. And characters that do not occupy one of those squares, characters that are only adjacent to a hindering terrain marker, will be dealt 1 damage and 1 damage only.

What happens to a Time Bomb that Tabitha placed on her turn if her special power is countered on her opponent's turn (before it deals damage at the beginning of her next turn)?
The hindering terrain square(s) will be removed from the map, just like the blocking terrain markers from Barrer are removed if Barrier is countered before the beginning of the Barrier character's next turn.

Can Tabitha Smith use the feat Armor Piercing to prevent damage dealt from Time Bomb from being reduced below 1?
Yes. Even though the damage is caused by hindering terrain markers (and not, say, by a direct attack from Tabitha), Tabitha Smith was the one who placed those hindering terrain markers to begin with. As such, the damage is dealt as a result of Tabitha and if she is using the feat Armor Piercing, her damage can't be reduced below 1.