Welcome to the board!
Whilst I think it unlikely (in fact, nearly impossible) for the Scottish to keep the Spaniards away from the colony, for the purposes of this thread I'll assume that somehow the Scots do - perhaps the Scots somehow get Lionel Wafer on-board and promise him any prizes he captures from the Spanish if he helps defend the colony.
This colony will suffer quite a bit, but if the Scots brought tents with them then it could've survived with a decent amount of people in it.
Scotland would still be poor after this, it spent (IIRC) a third of its entire wealth on the colony. Also I believe the goods that could've come from the Scottish colony may not have helped offset this, not to the necessary degree when you factor in the sheer cost of running the place - i.e. sending necessary supplies (though perhaps if the English were more lenient this would be less of a problem) and maintaining an army and a small fleet (again, maybe the Scots could ingeniously use privateers?).
The problem is that Spain wouldn't let this go, I mean a minor, northern country has just cut the entire Spanish American Empire in half, something that obviously couldn't just be allowed - privateers or no privateers. If worst comes to the worst I can see a Scots-Spanish War, the colony being destroyed and Scotland not only being further weakened, but utterly ruined. If the Scots are lucky England may get involved, with the monarch feeling one of their lands is being under attack thus calling on the other to help. If the English do help, though, I can imagine they'd demand either the whole colony itself from Scotland or they'd demand a cut of the profits - if there are to be any.