#1
I am having trouble getting the bass tone that I want for my songs. I'm using an Ibanez GSR205 and POD Farm in Reaper. Despite my efforts, the majority of the time it just sounds muddy and flat, like "wub wub wub wub." Not sure if it's my settings, or my playing, but some advice on this subject would be really useful for me. I like the bass tone in bands like Monuments, Periphery, Fit For A King.
#2
Split your recording of the bass in 2 tracks.
run the both through POD farm but without a overdriven sound.
After that EQ the Attack out of one track, so that you'll only hear the bass and not the pick scraping sound.
If that sounds wobbly just destroy the dynamics with a compressor or limiter.
you want to hear the flattest deep bass sound you'll can get.

in the other track you'll remove the deep bass sound, so that you only hear the pick attack.
add effects to your liking (compression, verb if you like, etc) and as last do a nice distortion or overdrive.
now adjust the volume of both the tracks and you'll have a lovely heavy/overdriven bass sound

I'm sure there are other ways, but this one works for me.

Also be aware of clipping, When picking insane powerfully the interface will start to cry.
so when you notice you are clipping just turn down the gain on your interface or on your bass guitar.

goodluck with finding your sound