Yep, E6000 is fine, it's another in the "goop" family of glues. I think it's really all the same product just in different packages. They sell their products in various niche markets: Crafters Goop (craft shop), Household Goop (grocery store), E6000 (Hardware store)... but I think it's all the same recipe. They certainly all stink the same! They all create a better bond than silicone for funky plastics and things that aquarium silicone won't bond.
I got the sliding glass E tracks in the mail today, it seems like normal plastic (not food container plastic) so it should be fine attaching to glass with plain old aquarium silicone. So If you didn't already buy the E6000 and already have Silicone on hand you should be fine. If you did buy it it'll do the job and then some.