well that depends, here are your options on swap and the corresponding ecu
OBD1 VTEC Swap
D16z6 Engine
p28 Ecu
OBD2 Vtec Swap
D16y8 Engine
p2p ecu
my recommendation to you is stick with an obd 1 engine and go with the d16z6 with p28 ecu.
if you stick with obd1 then to replace the ecu, you unplug your battery, unplug your old ecu, plug the new ecu in, plug your battery back in.
if you do an obd2 engine swap youre have some choices on what you want to do.
1.) keep your current obd1 engine harness, get an obd1 distributor and obd1 injectors, an obd1 > obd2 engine harness (obd2a if ecu is from a 96-98 engine, obd2b if ecu is from a 99-00 engine), and plug your obd2 ecu in.
2.) keep your current obd1 engine harness, get an obd1 distributor and obd1 injectors, get a p28 and plug it in to the harness.
3.) swap out the obd1 engine harness with an obd2 engine harness. everything is plug n play.
reasons why people stick to obd1 is because they have future plans for their car that require it to be tuned, and obd1 > obd2 for tuning.
hope i didnt confuse you too much