The job of a preamp is to take the input signal, eg. a mic or an instrument, and pre amplify it to line level. Once a signal has gone through a preamp it's going to be within an order of magnitude of line level pretty much (if the gain settings are sensibly set).
Most audio processing happens in this signal 'band', an EQ is designed to work around roughly line level so there should be nothing to worry about. Even if your signal after the preamp is about 1/3 of line level it should be absolutely fine and all working comfortably within spec. Line level is just a reference point really, and of course real world signals will be lower or higher than the nominal in almost every occasion. I don't think you have anything to worry about. You can always just push the preamp a little more to get a slightly better signal to the EQ.
Radically out of spec, ie driving the EQ directly from a guitar may have undesired consequences, but this would potentially be less due to the low level signal and more to do with the EQ not receiving a signal of expected output impedance more than something to do with levels. Even a very low signal with a near perfect (ie very low) output impedance should be processed satisfactorily with the usual EQ circuitry. Plugging a piezo mic directly into an EQ might sound odd, as although the EQ should be designed with a fairly high input impedance it is probably not expecting to receive a signal from a HUGE output impedance like a piezo mic's circuitry.
So for a preamp output interacting with an EQ input, you'll be fine even at significantly lower levels of signal, though if you feed it TOO weak a signal you might well run into other problems, usually a bit more low level noise because the EQ circuitries self-noise starts to become comparable to the level of the signal itself, but it really would need to be WAY too low for this to start being an issue with a half decently designed EQ processor.
But it sounds like the setup you have (though more clarification on exact setup, what you are amplifying etc. would be welcome) is perfectly correct and should perform well.
