You would take the train from Prague to Kutna Hora hlavni nadrazi, the main station.
From there you can take the tourist bus, which costs 35 CK.
Otherwise take city bus #1 which will drop you off around the corner from the ossuary.
Otherwise, you can walk, it is 2.5 kilometres and shouldn't take more than a half hour.
to get back
any of the above...or
train from Kutná Hora Město to Kutná Hora Hlavní nádraží
Easiest way is by train to Kutna Hora from Prague's Hvladni Nadrazi station.
Ticket office staff (it's a very swish ticket office!) speak enough English to organise a return ticket for you (very cheap).
Train takes around an hour and, usefully, your ticket will list intervening stations so you don't need to worry about getting off at the wrong place.
Having got off the train, turn right at the station exit, turn left just before the elevated section of the road and walk along the rather dreary main road until you come to a huge church on the left (Nanebevzeti Panny Marie).
Cross the road and either walk up the small road opposite, or do what we did and follow the signs (see photo) past a row of garages and along a muddy pathway to the ossuary.
It's about 10 minutes walk from the station to the ossuary.
To get into Kutna Hora proper carry on down the main road. It's a good way, though fairly easy to navigate, and takes around 35 minutes.
It's pretty easy to get to Sedlec from Prague - just get the train to Kutna Hora main station (hlavní nádraží), and then have a quick look at the tourist info map in the underpass in the station, this will show you where to go. It's probably a ten minute walk. There are buses from the station as well, but it's so easy to walk, why bother? You might want to consider the bus or a connecting train to the centre of Kutna Hora, but the bone church is nearer to the main station than the centre of town.
It is about 1km from the Train Station, and is towards the main town of Kutna Hora, as you past a large church to your right.. cross over the road and head up, and you'll find the church of bones ahead of you.. simple.. No need to go into Kutna Hora, and back out again if you only wish to see the Bone Church.