Ideas taken from EVE Online ship combat.
If we accept as a general premise that energy weapons and projectile weapons were not fitted to Isley ships, we can also safely assume that we are dealing with a relatively primative level of space technology, at least when compared to Star Trek. More along the lines of Firefly, we can assume a few things about ship technology:
1) Engines use a solid fuel, resulting in standard/conventional placement of engines at the aft of the ship, and making the burn-wake of the ship exceptionally hot.
2) Having been designed initially for exploration, the ships are unarmed, save for two points below:
2.1) A fore-mounted ramscoop, little better than an armored and angled bulwark to shunt or shatter debris in front of the ship during spaceflight.
2.2) Side mounted grappling hooks, for mooring the ship or hauling cargo.
General Ship Design:
Under the above premise, we can safely assume that all "weapons" are mounted on the port and starboard sides of the ship, as the entire front of the ship would be occupied by the ramscoop and armor, along with the bridge. The aft, likewise, would be entirely occupied with the engines and the jet-wake.
Assuming a lower level of technology than Star Trek, we can then determine that most targeting is done either via visual sight, but also via unguided magnetics. In short, grappling hooks from an attacking ship would be fitted with magnetic devices that once fired towards a enemy ship, would center in on their metallic hull. This creates a few interesting notes:
1) A smaller ship would, theoretically, have a weaker signature radius, thus making them harder to hit with grappling attacks.
2) Ship's sensors, such as they are, would function similar to sonar, save for the active return being based on magnetic signature as opposed to sound.
3) Clever navigators and captains can use natural phenomena to confuse other ship's sensors and grapples, either by the use of heavy metal asteriod fields and the like, or by using a planet's mangetic poles as masking.
I would like to introduce the idea of the transversal axis, a concept taken from EVE Online. In short, it is the axis around which a ship orbits in combat; given two orbiting ships attempting to attack each other, a successful hit becomes almost impossible. Under our given premise, the only decent way to attempt a successful hit is to position one's ship into a broadside, not unlike traditional sailing ship naval battles, as theoretically, a grapple would only bounce off the armor of a target is the degree of firing was under or over 45 degrees from the ideal 90-degree mark.
Thus, as can safely consider that ship combat would either be a matter of ambush and surprise, or something akin to space dogfights with each ship trying to out manuever or out-turn/orbit the other; once within the desired angle, grapples can be fired to attempt to drag the target ship off course.
As such, there's two methodologies to ship combat.
If in a boarding scenario, such as a one on one fight, both ships would angle for the best possible attack, and then reel the target ship into range of a boarding party. Most of the combat from that point is hand to hand on the enemy ship.
In the case of destruction, however, it almost requires a gang of at least three ships, two of which grapple the target and use their engines to counter-thrust enough to, essentially, keep the target in place. Once done, the third ship can either executre a 90 degree angle ram, or buzz over the enemy ship, burning it with their engines.
Weapons and Weapon Use:
Ramscoop - In an ideal ramming situation, the attacking ship will strike the target at a perfect 90 degree angle. This will catch the target on it's complete broadside, both protecting the attacking ship from the target's grapples (as they'd get pushed aside by the ram), as well as striking with the most impact. A successfully delivered 90-degree angle ram under a full burn should all but sever the target ship in half due to sheer interia, while leaving the attacking ship relatively unscathed as the already heavily reinforced ramscoop takes all the damage.
As a note, this almost requires the target to either be standing completely still, or grappled by at least two assisting ships to hold it in place.
Decompression Grapple Guns - Under the above premise, we can safely assume that the standard arrangement of explosive powder projectile weapons would not be an ideal in space conditions. As such, it makes a bit more sense if we assume that the grappling hook canons on a given ship would function under the idea of a air-lock decompression chamber. Air is pumped into the chamber to prime the canon, and then at the point of firing the grapple, the 'chamber' is opened, allowing the air in the canon to decompress, blowing out the grapple itself towards the target. Magnetic tracking and breach point explosives (see above and below respectively) complete the work by homing in on the target ship and destroying enough of the outer hull to lodge the grapple in the target ship's armor.
Breach points - Small explosive charges designed to create an outward facing explosion. Used either on the head of a grapple to breach armor and allow the grapple to find purchase, or once a ship has been pulled alongside, for a boarding party to make a large enough hole to breach the ship.
Boarding Parties - Under this premise, a boarding party would have to use magnetic boots to walk outside of their ship, walk across the cables connecting the two ships, and place a breach point explosive on the hull of the target ship - then using that hull breach to enter the target ship.