Markings appearing on the dergon are referred to as 'layered'; generally, markings appear over or under the others in a specific order: 

Nuance may affect the entire design.
Color mutations affect or cover the entire design.
Arcane and Radioactive markings may layer above or below all markings.
White and Black markings appear on top of the rest of the design, but may layer over or under other White or Black markings.
Dilution genes appear under White and Black markings, but over the rest of the design.
Most markings may layer over and under each other freely.
Flight appears under all other markings, functioning as a second base color. 

While not fully listed out on every marking page, a few Allowances tend to apply to all markings, unless they're specifically disallowed in the Restrictions, or directly conflict with the marking's description. The specific marking page overrules these!

Marking Break - especially near wings, markings may cut off in sections of the anatomy.
Multiple Edge Types - If a marking lists multiple edges, you may mix and match over the marking's coverage.
Small Spots - Especially with the Speckles free marking, small snips of color outside of the main marking are allowed.
Symmetric or Asymmetric - Your markings may freely show equally on both sides of the dergon, or be irregularly shown.

Soft edged markings may also cut off with a hard edge at anatomical points that would make sense. For instance, Sable does not have to fade into the wing on top of the back!

Most markings which are a lighter or darker shade of the base can affect the rest of the design, causing an overlay of darkening or lightening to change the colors of other markings. This can easily be done using Multiply, Overlay, or other layer effects- but be careful to not make the affected colors overly saturated, especially when using Overlay! 

Soft-edged markings such as Cloud can combine with the lightening or darkening effect as well, helping to give the entire design more texture and variation.

Additionally, if a marking with a darker than/lighter than rule is contained within the presenting range of another marking, you may optionally consider it to be darker/lighter than what it sits on, instead of referencing the chosen base color!

While some markings have specific combinations which allow extra options, most, if not all, markings may still touch and flow into each other. Markings being the same color, or overlapping with similar shapes, are allowed and encouraged. 

Especially in cases where markings present asymmetrically, you may wish to show a reference for the other side of your dergon! This is not required, but can provide a good official reference for markings such as Piebald.
You do not need an other side reference to draw your dergon asymmetrically! However, beyond normal variation, an other side reference will help with future art, as these are listed on the import and are on hand as a reference for others.

If you do provide a second side, markings may treat wings as symmetrical, or as having different dorsal and ventral sides. Both are perfectly acceptable, and markings showing on the dorsal side may gently appear on the ventral side. For Nyoomers, this is especially true, as the bottom wing can generally be considered to be showing the opposite side as the top wing. 

Markings shown on an Other Side ref should still obey their marking rules, and their shape does not have to match the main import side. Their layering, however, should match the main import; for instance if Blanket is shown covering Stripes on one side, Stripes should not appear over Blanket on the other! 

You don't have to provide an Other Side reference when submitting your dergon for approval; it may be added at any time via Import Updates! You also don't need an item to redesign your other side ref, and an other side update can also be submitted at the same time as a redesign of the main import image. 

Markings may freely mimic each other, especially in combinations. For instance, Cloud and Blanket paired might give an effect very similar to Sable.

Color Mutations such as Leucism or Silver should not be closely imitated, although similar appearances are achievable through the wide range of bases and marking color options. This is not very strictly enforced, but as a general rule of thumb, if a design's colors (including eye rules) are contained entirely within a mutation's allowed sliders, you may be asked to change it slightly!