a few threads for you to read

https://www.honda-acura.net/forums/s...=civic+keyless

https://www.honda-acura.net/forums/s...=civic+keyless

and a how to here
http://installdr.com/InstallDocs/Honda/PDF/466013.pdf

basically the stereo has the keyless controller in it, so you need to retain power to it for your keyless entry to work

you will wire up the new stereo like normal, then either splice or buy a jumper harness to wire up the stock hu with just a few wires, then you will hide the stock hu behind the dash or wherever you like

there are tons of threads and info on this, its a pretty common thing for people with 96-98 civics to do, and any car stereo installation place is aware of it

good luck, let us know if you need any more help