Originally Posted by Rockin Mike
If your amp has a builtin compressor turn it on now, it will act as a limiter to protect the preamp.
The rest of the post was good, but this part I wanted to address.
The preamp doesn't need protection, it will not be harmed by your bass signal spikes. Plus, the comp built in to most amps is not at the very beginning of the input section, so it won't necessarily even prevent distortion. It depends on the how any one specific preamp is designed, where the gain stages are, where the low-headroom stages are.
Generally, the comps built into amps tend to suck. There are exceptions certainly, but unless you have one of those exceptions, I would not recommend using them as a general thing. Even among the ones that don't suck, they tend to have a low ratio, so you have to set them to a bad, tone-squashing setting in order to limit big peaks. Consequently they are a poor choice for stacking with any other compressor. Recipe for bad tone and zero dynamics.
There's an article in the FAQ linked in my sig that explains "good settings" for a comp.
Also, while the Markbass will do equally well either in front of the amp or in the effects loop, most other pedals will not. Most other pedals only belong in front of the amp, not in the loop. Depends on the specific pedals and the specific loop though.