Programs for Chiptune

it's all on preference. with LSDJ, you get bass, samples, stock configurable waveforms, etc. with fami, you can configure for lots of channels, the interface is handier, you don't need to buy devices to get MIDI support, stuff like that. personally, i use LSDJ, but it all really depends on what you're comfortable with and what you compose.

i think you might like module style trackers instead of super bleepy bloopy ones. milky tracker, impulse tracker, that sort of thing.

i'm the worst at explaining this stuff

I started off with Modplug Tracker (OpenMPT), which is a pretty good multi-format tracker and fairly easy to use compared to most others of the sort. Milky is also pretty good, but as ant1 said, try many different formats/types and decide which one suits you.

With regards to your 2nd question, I've only ever used Famitracker so my opinion will obviously be biased. I guess it's a choice between whether I prefer the Gameboy or the NES; I think I'd go with the "smoother" sound of the NES.

Are you aware that you can use samples in famitracker? So instead of using another program, you could sample all your percussion.

whats wrong with not using chip drums and mixing it?

Get a drummer.

try one of the sample trackers like Milkytracker, you get full sample playback support plus you're not limited to the few chip waveforms Nintendo hardware provides.