A characters Animation Set is specified in its .fpe file.
Open any characters .fpe and you will find them listed at the bottom of the script.
The default set is listed in the manual.
In theory if making you own animations attached to your character models you can have any animation positioned anywhere within its range of frames and specify them in the entities .fpe.
In any AI .fpi file you choose to attach to the character to control its AI behavior say as its main file you call the named animation set of your choice from those you have listed in your .fpe - dependant upon what you wish the character to do at any given time.
e.g. :state=1,plrdistwithin=100:settarget,animate=2,rotatetotarget,movetotarget
Where animate=2 is a walk animation by default.
How such calling of various animation sets fits in to your characters .fpi script will depend very much on the circumstances.
One or two simple calls to animation sets that provide for relatively simple AI behaviours is not all that difficult to learn to achieve. If you require a single script to contain many variations of behaviour that string themselves together so that the character responds to varying circumstances relating to its environment or the player, particularly when forcing multiple behaviours one after the other or closely together in a manner that would mirror human behaviour where we are able to carry out more than one behaviuor at any time and quickly move to others is when AI in game engines becomes much more difficult.
Advanced AI sequences are not easy to produce in any indie engine.
To create your own animations sets for characters and get them to play correctly in FPSC - can pose some problem which may take a lot of effort to find a method for achieving - different to each user depeniding upon which modelling/animation progs they have access to.
Creating the animations is one side of the story - scripting the characters to use them successfully in a professional looking manner inside your game successfully requires a different set of disciplines and just as much effort.
I am sure there may be some users for one reason or another may have an easy time of this. For the majority it will be a great deal of hard work and the results can vary depending on numerous things including FPSC scripting limitations, some inflexibilities and some issues within the engine itself.
If you have spare time available then you will certainly learn a lot from the whole experience even if the end result is not quite what you may like to achieve.
I would suggest that as I have done anyone wishing to animate and script AI for themselves - start with some simple animation and scripting. Do one or two animations at a time and then create the script to control them when applied to your characters. If you can do that then once you find your method and perfect it - you can add animations and script further behaviours.
That way you can discover whats possible and whats not and decide whether or not the effort is worth the end result.
Or
You can wait for a possibility that TGC may extend the AI to meet with your needs.