Ive noticed that in one of my pairs that all of the pairs children had a visible trait that only one of the parents had as a carried trait. Would the other parent have to have that trait as a hidden carried trait or something else? This is all very confusing for me. (The pair is Shadow and Seaweed and the child I kept was Oliver, you can check my stables for reference.)

So I'm not the best at explaining things but I'll try to make this make sense. So since both Shadow and Seaweed have a trait in the gene three slot, they have a chance of passing either of those two traits down to the offspring. Usually it has to do with the letter associated with the trait. Since Pollen Markings is CC it is more dominate over the Iridescences trait (DD). So thats how Oliver ended up getting the visible Pollen Markings trait.

okay, so punnett squares help you work out what sylesti can pass down (you can see a more in-depth breakdown here-

When breeding, it randomly selects one of the two trait letters from each of the six slots from each parent, and puts them together with reference to the dominance (N>A>B>C>D>etc)

so offspring of
Shadow
G1: (NI) Mandarinfish
G2: (NN) None
G3: (DD) Iridescence
M1: (NG) Naga Armor
M2: (NA) Dragonfly Wings
M3: (NN) None

and
Seaweed
G1: (NT) Water Sprite
G2: (KM) Blue Ringed Octopus
G3: (NC) Pollen Markings
M1: (FI) Seashells
M2: (NN) None
M3: (NC) Naga Helmet

Possible combos of these traits:
G1: NN, NI, NT, IT (so 25% chance of vis mandarinfish, hidden water sprite)
G2: NK, NM
G3: ND, CD (50% chance of vis Pollen Markings, hidden irridescence)
M1: NF, NI, FG, GI (25% vis seashells, hidden naga armor, 25% vis naga armor, hidden sea fur)
M2: NN, NA
M3: NN, NC

(it's early in the morning so excuse me for only listing the names of the vis traiss)