So, the context of this post is referring to broken beat drum pattterns. The particular track I'm working on is Dubstep.
Most Kick samples from any sample pack will have a length between 1/4 note and 1/8 note, but for some tracks I feel the need to shorten them down to 1/16th note in total length to let my sub bass come in quicker and cleaner.

I side chain my sub bass to my actual kick drum so at 150 BPM with a Kick Sample that is nearly a 1/4 note, I feel like it doesn't let my sub come in quick enough. Is it a bad habit to shorten to length of my kick samples? Am I ruining the punch of my drums? It shouldn't really affect my transient except for the length... Just wondering suggestions and what you guys do if a kick sample is the right sound, but the release is too long to sit with your sub properly.

I also am wondering how to decide what exact point in a kicks transient do I sit on the one beat of every pattern? Is there an article anywhere about how to line up your transients properly on the 1 beat?

You really shouldn't be needing to adjust the length of the drum or use side chaining.

Consider the balance of the kick drum and sub bass.

Consider the lowest point cut off point of both the kick and the sub bass.

I'll tell you what i do to get a nice blend of sub bass and kick.

I typically get a good signal going in both, and then i adjust the volumes. I tend to have my kick drum higher than my sub bass.

I then consider the cut off point of my kick drum and sub bass. Since my speakers have a lowest point of 38 hz, i start making cuts that are in the 40-46hz range. Once i decide where my kick is set, i adjust the sub bass cut off point, a little higher than the kick drum, lets say in the 41-47hz range.

I also spend a great deal of time layering my drums (808, accoustic, physical modeler). That has EQ, and filters [in this order; low pass, high pass, higher pass]

Don't be afraid to put multiple eq's in a row to get a more filtered sound. That can also help you tie up some unruly ends.

This is also a pretty difficult thing to do. But once again, consider the volume bias of the two tracks and the eq cut off point.