Tom, i hope you mean the Seychelle filter and not the SiltStopper.
Anyways, Tom, in another Thread, Ben Tang is doing this very thing (read other Forum discussions on what the Seychelle filters and what it doesn't; also, search the Forums for Seychelle and see my Posts, and others too, about the efficacy of the Seychelle.).
The issue to make sure of before cutting your tubing is to make sure that the ID (inside diameter) of the tubing fits properly over the barb fittings of the filter (not too loose and is not too small to fit over).
Before cutting the tubing, remove the bite valve and see how the tubing fits on the Seychelle barbs. If it's a good fit, then remove it and put the bite valve back on.
Then, typically closer to the bladder, cut the tubing and insert the filter, paying attention to the gozinta and the gozouta sides of the filter.
Don't forget to "prime" the Seychelle per the Seychelle instructions before doing this. Did i leave anything out?
Don't forget to prefilter water into your bladder, so…
1) you don't too quickly clog your Seychelle (it can be periodically back flushed with the included flush bulb),
and…
2) so that whatever you use (chems or UV-C) to kill buggers too small to be filtered by the Seychelle, will work properly. Both chems and UV-C purification are greatly hindered by cloudy or turbid water.
Lastly, remember the Seychelle may not prove effective against all Crypto due to Crypto's flexible nature and ability to fold back onto itself (though, IMO, it will remove most, and possibly all of it). The Seychelle attempts to address this issue since it's a labyrinth filter, but theorectically some "folded" Crypto could still get through since "folded" Crypto may not exceed, or will be about, only one micron in size. Hence the need for chems (and proper dwell/wait time) or UV-C purification if this is a concern for you.
I don't see any reason why you can't use the Seychelle as an inline filter as you intend as long as you understand its limitations for inline filtering. It's probably better, by my way of thinking at least, to use the Seychelle in a gravity feed system with a larger pore siltstopper filter upstream of it to act as a automatic pre-filter for the smaller pore Seychelle. Then AFTER filtering and filling your bladders/bottles, chems or UV-C can be used to eradicate viruses/virii, bacteria, and recalcitrant Crypto (if any, managed to find its way through the labyrinth – not being familiar with how tortuous of a path this labyrinth is, i can't really guess how effective it might be on "folded" Crypto; i guess, one might say that theorectically, some could get through).
Hope this info helps.