Would it be necessary or a problem to use an overclocking application in conjuction with Apex 1.4?
Which is the best App for this ROM?
Where can I find information on the best settings to set everything at?
Necessary: Not, not really. There is no "need" to overclock.
Problem: No, no problem as long as you know what your doing.
I prefer jrummy's droid overclock app
https://market.android.com/details?id=com.jrummy.droidx.overclock There is an option in there under settings for "boot type" and you can select android service. This'll ensure that you do not overwrite any of the Apex startup files and will still provide you with overclocking on reboot.
Just be careful to test out any overclock settings you make before setting it to start on boot. If you pick a combo that locks up your phone, you can get stuck in a bootloop.
Fab also includes jrummy's overclock scripts in apex, so you can open terminal emulator and type:
su
overclock
then follow the prompts from there. I think you get the same stuff you get from the app, maybe you can't do custom settings, I can't remember since I use the app.