The higher a mods mk, the higher the base modifier for Primary and secondary stat bonuses will be.
When upgrading a mod each level increases the primary stat bonus, and every third level will either increase the quality of the mod and add a secondary bonus, or improve an existing secondary bonus if the mod is already the equivalent quality.
An A quality lvl 1 mod will already have 4 secondary bonuses, so will gain 4 boosts to secondary bonuses by the time it is level 12, but you will not know which bonuses will be boosted until you upgrade it. It could even be the same bonus that is boosted each time.
It's best to upgrade high quality mods with as many specific secondary bonuses that you want to maximise your odds of getting favourable boosts.
Once you unlock mod battles it is wise to farm suitable sets of low mk mods in the mod battles for your most important squad initially, which are also inexpensive to upgrade. You may sell these initial low mk mods or hand down to less used heroes as you farm better ones.
At that point you can work towards replacing those sets with maximum mk HP mods when you are able to clear the final tier HP mod challenge.
From there you will want to farm mods from more appropriate mod sets for specific heroes to improve on your existing maximum mk mods.
The initial max mk HP Mods you farmed before completing the other set mod challenges can be used later for crew members because the stats and set bonuses do not affect a fleets power, only the mk and level will increase a ships power.
Primary stat bonuses are the most important attribute of a mod.
For eg, a primary 5.88% HP bonus is higher than the equivalent 2.5% bonus an individual HP set mod will provide.
Primary stat variations are based on mod shape alone.
There are only 3 shaped mods with more than 1 or 2 primary stat bonus options, which are on the right hand side of your mod inventory; Arrow; Triangle; and Cross mods.
The most useful and hard to find primary mods are:
Arrows: speed/accuracy/crit avoidance/offense
Triangles: crit damage/crit chance
Bare this in mind later when farming for specific mod sets for heroes, particularly when a 4 piece set is required in order to pair with a 2 set piece you already have.
The second most important aspect of a mod is the secondary stats which is related to it's quality at level 1.
Boosted secondary stats can also exceed the equivalent mod set bonus, and can come quite close to some of the primary bonuses, as it is possible to have a secondary bonus boosted 4 times on an A quality mod.
So far HP% is the only secondary bonus that has been found on a mod with the same primary bonus.
The least significant attribute is the mod set.
Once you have enough maxed mods of one universal set like HP or Defense for a full squad, you can then move on and farm specific mods for each hero from other sets that better suit how you want to use any given hero, for eg; a 2 piece crit chance set for GS.
You can now also use the initial universal set to help unlock the mod challenge maximum tier battles required to farm the highest mk mods for what you want.
As mkV mods each cost around 450K to upgrade, it's best to not upgrade a mod until you have the primary stat version of that shape you want/need, and ideally with the mod set bonus you want, and is A quality at level 1 with at least 3 of the secondary bonuses you are looking for.
Once you have exactly the pieces with the ideal primary bonuses and set for any hero, you can try to improve your mods over time by finding rare high quality mods with ideal secondary stats for the ultimate edge from mod challenges and mod shipments.
Whilst shipment prices are high, if you find a very rare mod there, you could spend a lot more on cantina energy refreshes to never find as good a mod.
For a general guide check out:https://forums.galaxy-of-heroes.starwars.ea.com/discussion/1195/beginners-guide-its-all-about-the-tables
With the addition of fleets and both Plo Koon and his ship farmable with cantina energy it is now even more important to optimise your mod farming.