OP, definitely try putting the EF before your compressor to get the biggest dynamic range out of your signal. Also try using the Mix control, IIRC, to select only the up-sweep filter by turning it to all the way towards the up arrow.
I will say this, as others have noted, EFs are very personal and different ones sound and respond quite differently. I find the FilterTwin to be a relatively mild, atmospheric filter. Neither of the two filters (the up-sweep and the down-sweep) are particularly resonant, so the filters by themselves are not very wet or squelchy. It does have a nice mild volume boost which helps.
The other issue, about how it is dialed in for only a certain range of notes, is a common problem for EFs and it is two-fold. First, the notes with the most frequency content near the resonant peak of the filter are going to speak more. On the FilterTwin you can only control the frequency bandnwith the threshold, basically opening the filter more gets you up higher in frequency, but that is a crude control. The second part is that most basses do not have an even volume across their range. Since our hearing is most sensitive to mids, in order to sound balanced most basses have a louder low end. So as you move around the neck and across strings the amount you open the filter, for a given threshold setting, will change. If it sounds good low it can be hard to get the filter to move much higher up; conversely if sounds good higher up chances your low notes will slam the filter completely open and you lose the motion that allows you to hear the wah effect.
One other thing can really help: a little, very little, light overdrive. It adds harmonics, upper frequency content, which gives more info for the filter to process. Also many ODs roll off a bit of the lowest frequencies, making your signal a bit more balanced across the neck. You might be able to do this with your EQ as well, but I think it will be difficult to find a single EQ setting that makes both your EF and your unaffected bass sound good.
I find that I have to pick certain ranges to tune the filter for. This is one reason I like to have more than one EF on my board at a time. One is tuned so that it responds better to low notes, I use that for baselines and with the octaver. The other can be tuned for higher up the neck for solos and melodies.