To set up an XP/98 dual boot system you need to install 98 first then XP. XP will then overwrite the 98 boot sector with one of its own and set up the necessary boot files on the 98 partition.
You must use the Advanced Options of XP setup to specify the alternate hard drive. Otherwise it just upgrades the 98 system
It is possible to fix this afterwards. In theory the Recovery Console commands:
should help you sort it out.
However I have had mixed success with these and ended up copying the necessary files myself.
How did you get to your current position?