Here are the options that you have to configure Pokeballs on your server via GameUserSettings.ini. The defaults are shown below.

[Pokeballs]
DisableRescue=False
ChanceLifeModifier=1000
ChanceLifePercentModifier=1
HealingConsoleCooldown=0
EnableInArena=False
DisableOnWildDinos=False
UnconsciousCaptureBonus=30
CaptureFailedDefbuffTimeBase=10
PokeballPCTransferThreshold=6
DefaultPokeballSkinIndex=0
DefaultGreatballSkinIndex=0
DefaultUltraballSkinIndex=0
DefaultMasterballSkinIndex=0
HideProtectionBuffFromHUD=False
ExcludeCaptureDinoClasses=
DisableCustomUI=False

Here is an explanation of each. Any omitted options use the default value instead.

DisableRescue
- Set this to True to disable the "Rescue" feature of PokeballSickness. All other features of the buff will remain enabled, however.
Default Value: False

ChanceLifeModifier
- This is a value that is taken into consideration in the capture chance calculation. If this is set to 1000, then for every 1000 life the enemy has, 1% (see ChanceLifePercentModifier) is subtracted from the final capture chance.
Default Value: 1000

ChanceLifePercentModifier
- This is a value that works together with ChanceLifeModifier. This is the percent that is subtracted from the final calculated capture chance. See ChanceLifeModifier for more info on its purpose.
Default Value: 1

HealingConsoleCooldown
- The amount of time, in seconds, that users have to wait after using a HealingConsole. The cooldown timer applies to each instance of the HealingConsole separately, but is not user specific.
Default Value: 0

EnableInArena
- Use this to allow or disallow the use of Pokeballs in the Boss Arenas. This really only applies to Pokeballs (Captured), but it's not like throwing a normal Pokeball or even a Masterball would work on a Boss to begin with. :P
Default Value: False

DisableOnWildDinos
- If you like the storage idea behind Pokeballs, but don't want your users to be able to use them on wild dinos, then this is the option for you.
Default Value: False

UnconsciousCaptureBonus
- This is the percent bonus to the capture chance a dino gives while it's unconscious.
Default Value: 30

CaptureFailedDefbuffTimeBase
- This is the time (in seconds) that each stack of the Capture Failed debuff lasts for.
Default Value: 10

PokeballPCTransferThreshold
- Use this to change the threshold for when captured dinos are automatically transfered to your PC. Automatic Transfers will ONLY happen after a new capture, if you have a tribe-owned (or personally owned) PC in the world somewhere, and if you have this set amount or more of Pokeballs (Captured) in your inventory. To disable Automatic Transfers entirely, set this to -1. If you set this to 0, it will default to 6.
Default Value: 6

DefaultPokeballSkinIndex
- Use this to set the default Pokeball Skin for all players on your server. Each player can override this value by using the Pokeball Skin Selector tool. Use the chart below to find the index you want. Note, this option bypasses Admin-Only and Player-Specific skin limitations. If you set this index to that of an admin-only skin, all players will be using that skin. The same goes for player-specific skins. These are meant to be exclusive to a specific player (determined by me). Use this and the other associated skin index options wisely.
Default Value: 0

Pokeball Skin Index Map:
0 - Default
1 - Chrome
2 - Dive Ball
3 - Dream Ball
4 - Dusk Ball
5 - Fast Ball
6 - Glass
7 - Glowing Accents (Admin Only)
8 - Gold
9 - Halloween
10 - Heal Ball
11 - Level Ball
12 - Love Ball
13 - Lure Ball
14 - Luxury Ball (Admin Only)
15 - Metal
16 - Moon Ball
17 - Mystic Ball (Mystic Academy Only)
18 - Nest Ball
19 - Premier Ball (Admin Only)
20 - Quick Ball
21 - Rainbow Ball (Skin Selector Ball)
22 - Repeat Ball
23 - Rock
24 - Safari Ball
25 - Team Rocket's Ball
26 - Tek
27 - Wet Mud

DefaultGreatballSkinIndex
- Use this to set the default Greatball for all players on your server. See the DefaultPokeballSkinIndex for more info.
Default Value: 0

Greatball Skin Index Map:
0 - Default
1 - Chrome
2 - Glass
3 - Glowing Accents (Admin Only)
4 - Gold
5 - Halloween
6 - Metal
7 - Mewtwo Ball
8 - Mystic Ball (Mystic Academy Only)
9 - Rock
10 - Tek
11 - Wet Mud

DefaultUltraballSkinIndex
- Use this to set the default Ultraball for all players on your server. See the DefaultPokeballSkinIndex for more info.
Default Value: 0

Ultraball Skin Index Map:
0 - Default
1 - Chrome
2 - Glass
3 - Glowing Accents (Admin Only)
4 - Gold
5 - Halloween
6 - Metal
7 - Mystic Ball (Mystic Academy Only)
8 - Rock
9 - Tek
10 - Wet Mud

DefaultMasterballSkinIndex
- Use this to set the default Masterball for all players on your server. See the DefaultPokeballSkinIndex for more info.
Default Value: 0

Masterball Skin Index Map:
0 - Default
1 - Chrome
2 - Glass
3 - Glowing Accents (Admin Only)
4 - Gold
5 - Halloween
6 - Metal
7 - Mystic Ball (Mystic Academy Only)
8 - Rock
9 - Tek
10 - Wet Mud

HideProtectionBuffFromHUD
- Use this to hide the Pokeball Protection buff from the HUD if you want it out the way.
Default Value: False

ExcludeCaptureDinoClasses
- Specify a list of dino class names to exclude from capture. Any dino class found in the list will force Pokeballs (including the Masterball) to not work on them. Dino class names not always the name of the dino, so make sure you're entering the proper class name. You can find a dino's class name by viewing its spawn command. For example, the Reaper Queen's simple spawn command is this: admincheat summon Xenomorph_Character_BP_Female_C. The bolded portion is the Reaper Queen's class name. Enter all class names in a list, delimited by a comma for simplicity. The delimiter is not actually taken into account, but will help you with readability for future edits.
Default Value: Nothing. No dinos are excluded by default.

DisableCustomUI
- Allows you to disable the Custom UI if you plan on never using the feature and just want it out of the way entirely for your server.
Default Value: False