Two options: On or Off.
Do you have the skill? Yes, then you gain a bonus in situation X (maybe you get a bonus to your die roll, or maybe it opens up a new sub mechanism or game option)...No, then you just roll your flat attribute (or maybe you just can't perform this type of task at all).
I've played with this idea a few times in my game designs.
FUBAR basically does this...if you have a trait that's relevant to the task at hand, you add an extra die to your pool (conversely if you possess a trait that's detrimental, you either take a die away, or add a negative die if you're all out of positives).
Ghost City Raiders does this. The basic mechanisms simply get you to draw a card versus your attributes in a series of basic situations. New skills allow you to gain bonuses across a range of situations, or allow you to open up new situations.
Tooth and Claw does this, by simply allowing an extra die to be rolled if you've a skill appropriate to the task at hand.
There is an opposing school of thought when it comes to skills. The one which uses gradually developing skill mastery, or levels of ability within a skill. The problem I've had with that paradigm comes down to things like "literacy" as a skill...either you can read, or you can't. When you've got five (or ten...or more) skill level increments in "Reading: English", what is the real significance in increasing from one level to the next? Does your vocabulary simply increase? Would this simply be better modelled by an increase of intelligence?
This is another one of those things where the designers intention for the game is really made manifest through the rules they present to their players.
For the last few years I've liked games where the rules blend into the background. They facilitate play, make sense and move out of the way, rather than standing as overbearing guards at the gateway to narrative.
Just because I've liked that style of game doesn't mean I've been successful at writing it. The first game I published, "Platinum Storm" back in the early 1990's was meant to be a "lite-rules" game, and the whole thing fit into 30 pages (with character generation, a variety of character types, dozens of weapons and scores of equipment types, a basic magic system, and write ups for a dozen pseudo-Japanese provinces). Now it looks messy. It was a smooth system in play, but setting up characters to get to that smooth game play was a nightmare. That game used scaling attributes and skills based on percentile dice, the opposite end of the spectrum to where I now commonly sit.
My next published game "The Eight Sea" from 2008, was a collection of simple logical systems. Each one elegant, but when combined into a gestalt, they became very unwieldy. The actual play sessions I've run for the Eighth Sea have ignored most of the rules altogether, simply focusing on the card drawing mechanisms and the deck of the ship (which drives difficulties for the story). In that game I used two levels for every skill, "basic" and "advanced". It worked pretty well but got a bit confusing at times. It was after writing this that I started thinking of the "skills as switches" concept...what if two skills applied to the situation (could you add bonuses from both)...what about three?
It makes things easier to just say "Yes" or "No", rather than take the other path of applying synergies between skills and cross referencing one effect to see how it apples to another. I don't know if you could argue whether it's more or less realistic, but keeping things simple certain makes the story flow more easily (and thus aids in any suspension of disbelief throughout the adventure).
For Voidstone Chronicles, I think it makes sense to follow the skills as switches option. It fits the 8-bit gameplay style....either you've got access to "Weapon-type A" or you don't...either you can read magical incantations or you can't...either you gain a bonus with the local merchant or his prices are terrible.
The next things I'm looking at to really bring out the style of gameplay that I'm after are "feat trees". The simple combination of feat trees that open character possibilities and skills that simply give a yes/no benefit should allow for some great complexity of character while staying easy to manage.