You can replace or layer them.
Personally a big fan of layering stuff, am not a total chiptune purist but I like having the character of gameboy drums reinforced by other drums.
Layering stuff is basically about getting different elements of a kick/snare from each layer.
So if you've got a noise snare for example, it might be lacking a punchy snap on the beginning or some body...
So (for example) maybe find a really snappy snare to put underneath the LSDJ one and change the envelope so you only really hear the snap of it. Balance the volumes up, maybe compress the two together a bit to gel them and hey presto: what sounds like a gameboy snare, but punches through the mix a bit better.
Or maybe your LSDJ kick sounds great in the mid range, but lacks a bit of weight - maybe grab an 808 kick sample and layer it underneath - so EQ the higher end of the 808 and adjust the envelope of the sample so it decays the same way as the LSDJ kick. Again - adjust volume, maybe compress them together (don't make the attack of the compressor too quick or it'll affect the low end) and you get a kick that sounds like it came from LSDJ, but has a load more low end.
the possibilities are kinda endless - the key is to have an aim in mind when you add a layer and to EQ/envelope out anything that isn't helping you add what you want to add. Layering claps under snares often sounds pretty amazing (actually 808 samples are a good way to hear this as the snare sound feels almost like it's lacking the clap in the first place, but the two together sound GREAT.
