myfist0, upon learning of the variety of species 8472 ships, I hereby declare you must include Species 8472 into your arsenal for your SotC mod.
Things to know:
Species 8472 will not have the same numbers of ships or structures as the Vanilla Sins races. They don't even have the same number of ships as their Armada II Counter parts. They aren't underdeveloped in Armada II; they simply don't have that many various ships. In armada II, they possess about 75% the amount of ships as the other races, and about half the structures.
Species 8472's Starbase will be mobile, on par with the Orkulus, with similar upgrades.
species 8472 builds ships in Vacuum space in 2 ways.
One way is through Embryos. There are two types of Embryos: The passive and active Embryo. They must possess the ability to construct the ship, like the Starbase Constructor in Entrenchment.
The second way is gating in ships that are especially construct (much in the same way a Galaxy class ship is constructed), but this can only be done in fluidic space. This is generally for large ships only; Battle Frigate (capital), Battleship (Capital), Behemoth (Capital). Their three capitals will fill the 5 roles usually filled by vanilla races.
In Armada II, Species 8472 used only biomatter to construct everything. They had no population, crew, capital crew, dilithium, or metal. Armada II isn't canon, so we can just go with Credit, Metal and Crystal.
With these things said:
Capital Ships. Species 8472 has no fighters; end of story. They will be at a severe disadvantage in this respect. But they will possess a variety of abilities that will either target fighters, or nearly nullify fighter damage. With that said, 8472 will have the following niches of Capital ships: Battleship, Colony, Support.
Battleships, Battleship
Telekinetic Strike - Single hit damage
Rapid Regeneration - Increases already fast regeneration
Insanity - Like disorientation, very low AM cost, medium recovery, long duration. Single Target, not channeling.
(Super) Planetary Pulse - Massive Instant Damage to Planets for no AM cost, long cooldown.

Colony, Behemoth
Colonize - Colonizes
Nebula - Generates a Nebula field, preventing jumps, quickly destroying small objects (strikecraft, bombers).
Rift - Allows the Behemoth Initiate a phase jump from any location.
(Super) Nebula Reaction - If the Behemoth has enough power left, or another Behemoth is present, it may fire a pulse into a Nebula field to deal massive damage to all enemy ships in the field.

Utility, Battle Frigate
Concentrate - Better focuses weapon fire on target, at least doubling damage upon target. Channeling.
Planet Concentration - Planet Bombardment damage is multiplied similar to Concetrate.
Rapidity - Syncs the Frigate with allied ships, significantly reducing phase jump time within a field.
Regenerate - Immediately places Shield and Hull back to 100% but costs 300 AM.
Smaller Vessels: Species 8472 doesn't do very well to distinguish between Frigate and Cruiser. Instead, they have ships which can be build in vacuum space from Embryos, and are very small. These are all built from Active Embryos.

Scout, Scout
Detect Cloak - This vessel can make invulnurable targets vulnurable, and detect mines for targetting.
Telepathic Link - Replicate TEC scout ability.

Long Range Frigate, Destroyer
Read Computer - The Telepath aboard the Destroyer telepathically reads the enemy computer in range. You immediately detect which planets they own.

Heavy Cruiser, Cruiser
Psionic Disruption - Disables and makes invulnurable one target. Nonchanneling, Duration = Cooldown 20=20, 30 AM?

Anti-Module, Launcher
Can target enemy ships as well.

Support and Anti-Module, Collector
This ship has not direct firepower, and mainly is used for boosting resource income. It does have military purposes, though.
Mining Beam: Target any Planet or minable asteroid to gain an instant single bonus of Crystal and Metal.
Extraction Beam: Deals moderate damage over time and provides credit and metal upon completion.
These are produces from Passive Embryos.

Support Cruiser, Transmuter
This ship has no direct firepower, and mainly is used for boosting abilities and most commonly assists the Collector. Ths ships naturally repairs itself faster than anything else known to exist, and should have an extraordinary Antimatter Regeneration rate, aswell.
Assistance: Reduce Ability cooldown and antimatter cost. Single Target, nonchannel. High duration, low cooldown.
Refuel: Consuming 100 Antimatter, this ship provides 100 antimatter to a target. Medium cooldown.

Capital Ship factor, Fluidic Gate
This should have an inaccessable stable build from constructors, but therwise also be buildable from passive embyros.
They port in Battleships, Behemoths, and Battle Frigates.
And these three beauties are also built from passive embryos.

This is the most basic research station, and Likely best used as the Civilian Structure.

This is the structure used in Armada II to upgrade the Behemoth, but it can be used for something else.

This is the structure used to upgrade ship systems, ie: combat, hull/shield, sensors. This would pull off being the Military Lab.
See the loose ends here: http://gaming.trekcore.com/armada2/ships-species8472.html
Things like the Defender can be the construction ship.
Sentinels would take up being Turrets. Please don't forget that they are very powerful turrets relative to the other turrets in Armada. One Sentinel takes out the Federation Sovereign class Battleship easily.
They also have mines. A glance of active and passive embryo are provided within.