Full Tilt No-Limit Hold'em, $0.25 BB (5 handed) - Full-Tilt Converter Tool from FlopTurnRiver.com

saw flop | saw showdown

SB ($2.90)
BB ($120.95)
UTG ($10.10)
MP ($27.85)
Hero (Button) ($54.20)

Preflop: Hero is Button with 3, A
UTG calls $0.25, 1 fold, Hero raises to $1.25, 1 fold, BB calls $1, 1 fold

Flop: ($2.85) A, 6, 3 (2 players)
BB checks, Hero bets $2, BB raises to $8.85, Hero raises to $23, BB raises to $119.70 (All-In), Hero calls $29.95 (All-In)

Turn: ($108.75) 6 (2 players, 2 all-in)

River: ($108.75) 2 (2 players, 2 all-in)

Total pot: $108.75 | Rake: $3

I'm not sure whether stacking off with two pair is the correct play, especially since we're so deep stacked. Villain seemed to limp a lot and raise little, so I didn't put him on much of a hand - something like an ace and good kicker. I usually play FR (and this was a full ring table) and since a few players left the table in this orbit I've not left yet.

I don't have experience short handed and I was wondering if anyone here with experience shorthanded would play this differently?