What effects do resources have

The difference is in the ships and number of troops.

Naval troops are fewer than their land equivalent, making them weaker as a result. However, naval ships are far more powerful than transport ships and also come in several variations.

Some of the ships can destroy an enemy transport by ramming it only once even frontally, others can be particularly fast, allowing you to flee from or intercept any transport ship. Also, siege ships built in the harbour actually have siege weapons. A siege transport on the other hand only transports the troops that man the siege weapons, making land siege units pretty useless in naval battles; similarly, a cavalry transport only contains the riders, not the mounts; such ships cannot be built however and only exist as transports.

TL;DR

Transports:

• Have more troops, and are therefore more suited for boarding.
• Have weak ships, and should therefore avoid being rammed.
• Do not allow the use of siege weapons or mounts, which need to be protected at all costs.

Military ships:

• Have stronger and faster ships, making them ideal for ramming or hit-and-run tactics.
• Have special skills, which transports don't.
• Can use siege weapons, giving them a significant advantage over very long ranges.

The screenshot shows 3 different auras, here is what each are and what they mean:

The character to the right only has one aura, which is red: the red aura only appears on characters that have the red skull above it, which represents attrition damage, see this answer.

The character to the left has three different auras, one of which is barely visible (notice the red aura at the unit's feet). The white aura replacing the red one, which is surrounded by Rays of God only appears on characters which you are currently inspecting by left clicking on it.

The last visible aura in the screenshot is the white circle of light at the unit's feet. It only appears on units that are currently in the "Forced March!" stance, allowing them to move twice the usual distance on the overworld map at the cost of not being able to attack (they can still defend, however), as well as penalties in field of view and morale during combat.
Fleet have the same aura for their own version of "Forced March!", which is called "Double Time!", as well as a similar aura for their "Patrol" stance, which is a white circle of vapor floating above the fleet.