Nice rig. +1 to starting out 'flat' with the filters off.
If you aren't familiar with the logic of the filters, here is the scoop:
VPF.. this is the typical 'enhance/contour' type filter, similar to those found on the Eden, GK and Thunderfunk amps. It is an 'all in one' tone control that simultaneously boosts and extends the deep low end, softens the lower mids, and boosts and extends the upper treble. Hence, the term 'scoop control' used by many. While this control can be a nice way to smooth and open up a very mid voiced cab like some of the small Schroeders (as an example), a little bit goes a VERY long way. I can't imagine every turning that filter past 9 o'clock for any reason with any cab, and with most cabs, you would never use it at all.
VLE.. this is a unique control not found on other amps. It is a variable lo pass filter. What this means is that, as you turn it up, it doesn't really boost or cut anything, but rather, it gradually takes a fixed amount of upper level frequencies out, impacting lower and lower frequencies as you turn it up. So, at 9 o'clock (for example), it cuts just the very upper end of your treble response, making your tweeter sound more 'paper cone... hence the term 'vintage speaker emulation... VLE. As you turn it up to noon, you have cut everything above the mid mids, given almost any cab a sort of 'old school 15' type vibe. Pretty cool used sparingly.
My guess is, the head set flat with your cab, with a little VLE to control the top end if you don't dig the zing, and possible a touch of upper mid cut around 1K (that would be the yellow hi mid freq knob at around 1 o'clock and the black hi mid level knob around 10 or 11 o'clock) will sound darn good for a clean, punchy, warm tone. Of course, if you want grind or distortion, you will need an external pedal like the VT pedal from Sans Amp.
This is my favorite head. I have many clips of it on my Youtube channel, with different cabs and basses if you want to get an idea of what the head can do!
Enjoy that rig... and go easy on those filters!

Another tip... the F500 preamp is designed to run clean. You should set that at a level just below the clip light coming on. To get the most open, clean tone, you should never, ever see that clip light... it isn't a 'warning' light, it is an indication of too high of an input setting. The Bongo is a pretty hot output bass, so I assume you would set your pre gain control well below noon, depending on how hard you play and how much bass you roll in with your on-board pre.