I strongly advise starting whilst riding the mount, this can avoid almost every bug involving horse riding. Starting in ride mode whilst dismounted can occasionally cause you to jump to the horse's location or have you mount and not move. The majority of the time I have tested starting dismounted, I tend not to have any issues - the player mounts and rides as they should. The not moving bug is resolved very simply by starting again. This is why using the quickstart hotkey is incredibly useful. 

If you do not have a horse, using start will summon a unique, invulnerable (and speedy) horse named Fish who can be found outside Riverwood. 

Despite having speed settings, the actual speed of the mounted travel can be largely affected by the speed of the mount itself. If you have a mount that moves very quickly, it will be faster than average. Take this into consideration when using mods such as ridesharing, gypsy eyes caravan, etc; where using lower speeds may be beneficial! Using higher speeds, however, is a great way to avoid combat! 

Use stop and dismount if you want to dismount at any time.

To enable walking mode, go to the MCM > Misc. > Enable Walking. You can enable walking mid-journey. Walking mode allows you get closer to NPC, engage in combat and also go through doors - such as if you're following an NPC and they suddenly go into an inn, you can go in after them. Walking, however, can give trouble getting up hills! Grr!

Learn all three words of the bend will shout from DLC2. Use bend will on a dragon. Mount the dragon as you normally would and then use SkyTrek. Everything else works as it does in vanilla. Do not use SkyTrek's stop button, just stop how you normally would and wait for the dragon to land - it can take a while!
If bend will mounting works on the dragon, so will SkyTrek. If the dragon is mounted via other methods (such as the fully flying dragon mod) then I can almost guarantee this will not work.

Automated combat can be enabled on the MCM combat page. I recommend enabling it, but only when walking. When the player is attacked with it disabled, the player will just stand in place and not respond until the enemy is dead. Only enable shouting outside of combat. You should also avoid changing combat class in combat. You can, however, stop SkyTrek mid-combat and change class then start again - just make sure you are properly equipped before starting! Note: Autocombat is not active in either life mode or when riding a dragon, you can still attack when dragon riding the same as vanilla.

When combat is enabled, you will automatically retaliate to an attack. If you are not directly attacked by an enemy, you will continue with your journey. This is deliberate as automated player combat is nowhere near as efficient as an NPC - Autocombat is an "act when necessary" situation. However, equipping a follower with a SkyTrek ring will cause you to react to any hostiles that attack them. The player can continue to attack after a target is dead and will only focus on one target at a time.

After enabling combat you have a few "classes" to choose from that dictate how you behave in combat. You can also enable shouts, each class has its own shout. They are as follows:

Warrior (Default)

Shout: Ice Form

The melee class. If shouts are enabled, will fire off shouts frequently. Ice form can turn your followers into a block of ice without Companion's Insight.

Mage

Shout: Fire Breath

The magic class. Due to restrictions, the player only uses the right hand and the spell(s) is/are chosen automatically. You can't choose the spells. Mage comes with a major warning in that it may choose a spell which may in some way harm/kill the player. Such as an explosion.
The mage class, due to restrictions and risks, is best used for travelling alone or after obtaining the DLC2 ability "Companion's Insight".

Ranged

Shout: Cyclone

The archer's class specialising in dealing damage from a short distance. I recommend using ranged only if traveling with followers/summons etc. For the ranged class to work correctly, you need to be able to maintain a short distance between you and your enemy. At an optimal distance, the player will fire off shots fairly frequently. If enemies are too close the player will try to gain distance and may not fire. The player may also hold fire if the target is out of range. The player should only use this class in a situation where distance can be maintained. Ranged can take a while to go back to a non-combat state even when not attacking. 

You do not need to have learned any shouts to use them, but shout mode is intended for later game use as they can be OP early game. The shouts are silent, this is not a bug.

SkyTrek can be used with cart mods such as Gypsy eyes, dragonkiller cart etc if it is used in a very specific way.
Use the following settings before doing anything:
Autocombat - Disabled
Walking - Disabled
Speed - Walk (not necessary, but recommended due to cart physics!)
To use SkyTrek with a carriage mod:
1) Mount the horse. Not the carriage.
2) Start Autopilot
3) Enjoy the trip
4) Stop and dismount when done.
Repeat the above each time. Use the mod's system as you normally would and just use autopilot while you are riding the horse. 
Important note: You cannot quick start and auto-mount the hitched horse if it is your last ridden horse - ie you just got off the cart, didn't ride another horse and quick started. You'll need to switch to the walking mode or ride a different horse before quick starting after using the carriage.

Mod added lands or locations can work with SkyTrek's radiant system "out of the box". Provided a new world or location is correctly keyworded, it should be usable by the radiant system. Even if the radiant system is not working in a new land, you can still use the custom marker! Mod authors wanting to make a location compatible please see the mod author section!