A lot of what you're describing really doesn't sound like Pro Tools qwerks or issues, more or less just mixing/engineering things.
To get your kick to stand out, you can do one or more of many things. If you have headroom, pull the fader up and boost the level. Otherwise, try adding some slight compression, and EQ. Use a parametric EQ and try boosting 2 or 3 dB, medium Q (bandwidth) at around 60Hz to get a thicker deep bass sound to it. If you want more of a boxier kick sound, try boosting around 100-120Hz. Play with the frequency/bandwidth knobs. Another thing you can try to do, is layer a few more kick samples overtop of your first one. Try different combinations of kicks you like, but also, try putting some other kicks you may not necessarily like by themselves on top. Maybe a very short, transient heavy kick on top of a longer, more sustained 808 type kick to give it that punch. You have almost an unlimited amount of options when it comes to layering sounds.
Also, one thing you may want to do, is....ahem, Upgrade you're Pro Tools! lol...There features available in 6.9 are SOOOOO worth the upgrade. I mean, 4.7 is ancient lol. Better plug-ins, beat detective, strip silence...All kinds of stuff
If you have more detailed questions, just hit me up PM, and I'll try my best to help you out.