Well The way I started modding was by editing the files directly as its easier and allows for more, and then making a mod later.

So to change a Populations Splicing bonus you would want to edit the %Install Location%\Endless Space 2\Public\Simulation\SimulationDescriptors[Population].xml File.

The Particular Bit you want would be around line 1235 (as of patch 1.0.18)

<!-- Mavros -->
   <SimulationDescriptor Name="ClassPopulationAssimilatedEmpireAffinityMavros" Type="ClassPopulationAssimilated">
         <Modifier TargetProperty="PopulationsAssimilated" Operation="Addition" Value="1"Path="../ClassEmpire" TooltipHidden="true"/>
   </SimulationDescriptor>
   <SimulationDescriptor Name="ClassPopulationAssimilatedPlanetAffinityMavros" Type="ClassPopulationAssimilated">
         <Modifier TargetProperty="BonusPopulationIndustry" Operation="Addition" Value="2"      />
   </SimulationDescriptor>

The First Part you need to worry about the second part is what defines the bonus from Splicing them, Changing the Value changes the amount and changing the TargetProperty changes the what type of bouns is given (in this case its industry) All the other Assimilating bonuses are also in this file.

Now Modding the Population's Base Traits is quite diffrent.

Each Minor faction population has two traits that define the bonus yields they provide 

E.g. Mavros have the +1 Industry Trait (PopulationModifiersTraitPrimaryIndustry in the files) and the +2 Industry on hot Trait (PopulationModifiersTraitSecondaryIndustryHot in the files) 

The Difficulty in modding these is that more than one minor faction population uses the same trait. In this case the +1 Industry Trait (PopulationModifiersTraitPrimaryIndustry in the files)

Is used by not only the Mavros but the Bots, Remnant & Pulsos so any changes will apply to all these factions. 

lucky also in this case the +2 Industry on hot Trait (PopulationModifiersTraitSecondaryIndustryHot in the files) is only used by Mavros

Refrences as to what minor faction use what trait can be found in the ...\Public\Simulation\PopulationDefintions.xml File

The Mavros can be found around line 694 (as of patch 1.0.18)

<Trait Name="PopulationModifiersTraitPrimaryIndustry"/>
<Trait Name="PopulationModifiersTraitSecondaryIndustryHot"/>

Now before you can actually edit these traits you want to go to the ...\Public\Simulation\PopulationModifiersTraits.xml File

and find their SimulationDescriptorReferences (This is at line 873)

<PopulationModifiersTraitName="PopulationModifiersTraitPrimaryIndustry"SubCategory="Primary"ShowInCustom="true" Cost="5"><!--Local Bonus: Craftsmen-->
      <Modifiers>
          <ModifierClass="ClassPopulationEmpire">
               <SimulationDescriptorReferenceName="WithPopulationPlanetModifiersTraitPrimaryIndustry"/>
          </Modifier>
          <Modifier Class="ClassPopulationPlanet">
               <SimulationDescriptorReferenceName="ClassPopulationPlanetModifiersTraitPrimaryIndustry"/>
          </Modifier>
     </Modifiers>
     <AssimilatedModifiers>
          <Modifier Class="ClassPopulationPlanet"><!--Bonus given to the Population that assimilates them-->
               <SimulationDescriptorReferenceName="ClassPopulationAssimilatedPlanetIndustry"/>
          </Modifier>
     </AssimilatedModifiers>
</PopulationModifiersTrait>

so here we have WithPopulationPlanetModifiersTraitPrimaryIndustry , ClassPopulationPlanetModifiersTraitPrimaryIndustry and ClassPopulationAssimilatedPlanetIndustry

So now we can actually edit these traits, you now go back to the ...\Public\Simulation\SimulationDescriptors[Population].xml File and search for the relevent traits

Now the Populations yield bonuses can be found in the <!-- Local effect increases --> section (line 1657)

<ModifierTargetProperty="BonusPopulationIndustry" Operation="Addition" Value="1" Path="WithPopulationPlanetModifiersTraitPrimaryIndustry/./ClassEmpire/ClassColonizedStarSystem/ClassPlanet/ClassPopulationPlanetModifiersTraitPrimaryIndustry" TooltipHiddenIfPathInvalid="true" />

Just edit this line to change the effect of the trait.

I'm going to leave it there for now, if you want for detail / help in a particular area just ask (I do normaly respond quicker, I just have been occupied with moving house since before this was posted)

Edit: I have seemingly somewhat broken the forum styling (on my screen atleast) with the runaway text