I'm a drummer turned bassist. I know sticks, heads, shell sizes, cymbals etc. Soundgear is still new to me and trying to remain a mystery so pardon ignorance and let me ask a sincere question. I have a bass with two pickups and a 3 band equalizer on board. I have a GK Fusion 550 with so many adjustments it's crazy. Why would I and what would I do with more control options offered by pedals????
It begins with the sound you're after and the sound and style of your worship team. Pedals don't have to be complicated.
For a basic clean sound, something as simple as a just having a compressor pedal is enough. The compressor evens out the volume differences in your playing, makes your picking, slapping, and finger style sound more consistent and even. I like my MXR Bass Comp, it was my first "expensive" pedal but it's my "always-on" pedal now.
After that some people like to be able to fine tune their EQ. Whether it's to tighten their bass sound, cut through the band mix better, or to enhance the tone of some other effect further down the chain. There are pedals that do this, and allow the EQ change to be activated and deactivated via foot switch.
Last in the clean setup is a good Preamp/DI like Tech21 NYC, or the Boss BB-1X, or the Aguilar Tone Hammer. This allows you to send your signal to FOH unaffected by your stage rig. It can be necessary if your stage rig affects your bass signal negatively (adds ground noise, stage EQ might sound terrible through the house system, etc). I had those two problems bad.
That's just for a clean setup. You could add a tuner pedal that'll mute your signal while you tune, an added convenience.
Further on down the line, other effects come into play. Effects like overdrive, chorus, and delay all have their purpose; think of it as painting with a more elaborate palette of colors. Effect pedals allow you to be more creative with your musical self expression. Within a band setting, effects can help to tie the band sound together. It boils down to whether you like what you hear, and whether it works with your team's style.
This is an example of how I use my effects. This weekend we played Chris Tomlin's Sing, Sing, Sing. We play it as a pop alt rock tune so I used my Bass Soul Food overdrive with my neck pickup. I had a thick p-bass style tone with a bit of overdrive. Next was How He Loves by Crowder, straight clean soloing my bridge pickup for more of a jazz bass tone, with bass boosted all the way on my Preamp. Never Stop by Urban Rescue, it has a strong driven rock vibe the way we play it, so I used my OBD-3 because it's setup to have a heavier overdrive with some bass boost. Soloed the neck pup and ask the guitarist for a pick. Sounded awesome. Last was Praise You In The Storm by Casting Crowns. Both pups on, clean with a bit of bass and treble boost on my onboard Preamp. All the while, having my compressor on and having my Tone Hammer engaged with my choice of EQ settings on it.
Effect pedals are fun but not necessary. I tried to be thorough with my explanations so i hope it helps.