First I am assuming that since you approached the idea of stacking them they are in a location close enough to utilize the stackwise technology?
So are these 2 switches connected with one uplink or 2?
Are you only using the one vlan or are you using mulitple vlans with ports in those vlans?
To assign an address to a pure L2 switch you need to put an IP address on interface vlan 1 or the management vlan of your choosing. I would reccomend staying on 1 because you have little knowledge of L2 switching. I would reccomend you apply an ip to both switches for ease of management. You would also have to open up your vty lines for some type of remote access as well..(telnet, ssh, ect)
switch#(config)int vlan1
switch#(config-int)ip add x.x.x.x x.x.x.x
don't forget no shut on interface....!
If there is only 2 switches I would not bother with the stackwise, but thats just me. its just as easy to configure both for management.
When you say manage, are you talking in the sense of NMS (network management system) or just basic configuration...??? There are products out there such as HP Openview, CiscoWorks, or WhatsUpGold, that allow you to see the "big Picture" but they can be costly. If you only have 2 switches then there are free tools that are available if you look.
As far as preferred method, there are more than one way to skin a cat. How many users do you have on either switch, fully populated? You can trunk the 2 switches together using a L2 etherchannel to maximze the size of your pipe if the need is there but if not then a redundant connection between the 2 switches will be sufficient. If you can not afford the time that STP will take to converge then you could start looking into things like uplinkfast.
As many details as you could give about your network without revealing too much then post it.