He's short so, "well, get it in, I might have fold equity."

I just wrote a tonne about this hand and realised I played it pretty terribly: his range consists in 9x, two pair and maybe strong-x 5x and 6x type hands, with the odd pocket pair thrown in, so i've got a little but not a great deal of showdown value.

It's like almost an instant thing - he shows weakness on a turn card I might represent so i'll just stick it in and expect him to fold a lot. But he's probably not folding 9x type hands come to think of it. However:

Can I raise if the flop is 2-tone? In the hope that he calls without the right price to do so or if not to simply protect my hand when i'm ahead more often?

PokerStars No-Limit Hold'em, $0.25 BB (9 handed) - Poker-Stars Converter Tool from FlopTurnRiver.com

MP2 ($25.65)
MP3 ($14.50)
CO ($33.05)
Button ($23.15)
Hero (SB) ($25)
BB ($4.75)
UTG ($8.65)
UTG+1 ($24.65)
MP1 ($31.10)

Preflop: Hero is SB with 8, 8
5 folds, CO bets $0.75, 1 fold, Hero calls $0.65, BB calls $0.50

Flop: ($2.25) 5, 6, 9 (3 players)
Hero checks, BB bets $0.75, 1 fold, Hero calls $0.75

Turn: ($3.75) K (2 players)
Hero checks, BB bets $0.25, Hero raises to $3.25