"Tube sound" is vague for a number of reasons, but mostly because it depends on how *you* define it: a little bit of overdrive, a lot of overdrive? Some bassists don't want any overdrive, they just want harmonic richness.
So, just tweak the knobs (Gain, Master, Drive, Tube Gain, and don't forget the Pad switch) to whatever sounds best for you! If you like overdrive, then don't worry about the clip light: it's not a danger indicator. I got great overdrive sounds from my 3Pro by turning up gain so that the clip light was flashing almost constantly. In fact the clip light would often flash for some of my cleaner tones.
And the "Tube Gain" control is just another parameter. Don't feel like you *must* have it fully CCW to maximize tube tone.
Bottom line, let your ears decide, not your eyes. Again, just turn the knobs until you're happy.
P.S. One thing you might want to worry about is the graphic EQ. It's solid state and sounds like utter crap (IMO) when clipped. I always bypassed the graphic EQ completely.