Hi,
switchport trunk native VLAN 99
on bot trunk sides.
See http://www.cisco.com/en/US/docs/switches/lan/catalyst2960/software/release/12.2_50_se/command/reference/cli3.html#wp1948736
To change the management VLAN you need to configure an IP address for int VLAN 100.
See "IP address" section in the same document, just replace int VLAN 1 in the example with int VLAN 100.
Just be careful, you could lose your switch connectivity when changing the IP address remotely.
If you are moving to a new subnet, you might need to change the default gateway, too, which might be tricky when the switch is placed in a remote site, e.g.
BR,
Milan