You have each OS in its own partition/drive. Logically - unless you 'deliberately' arranged/chose to share a common pagefile.sys - there will be one on each partition for the OS resident there. (I doubt you chose to share a common pagefile.sys - few folks do - so I wouldn't worry about it in your situation occasion.
It isn't critical to lose the W2K pagefile.sys; it can be left and will more than likely be replaced by W2K server 'version' during setup. It's your choice - if not sure/comfortable, then leave it be and just delete the c:\winnt folder...
What to delete in the boot.ini?
Typically in your boot.ini you will have a couple of lines similar to the following:
multi(0)disk(0)rdisk(0)partition(7)\WINNT="Microsoft Windows 2000 Professional" /fastdetect
multi(0)disk(0)rdisk(0)partition(9)\WINXPPRO="Microsoft Windows XP Professional" /fastdetect
These two lines are from a multi-boot system that includes W2K-Pro and XP-Pro amongst other OS.
If deleting the W2K entry from this boot.ini then it would be that first line (which refers to windows 2000). You would not delete anything that refers to XP (and in your case it would probably include " windows " (with/without "" ) in the line. (My XP-Pro entry is flagged/labelled as WINXPPRO - I like to make things clear for my grey cells...)
If you have the W2K recovery console installed there will be a line for that too (it can also be deleted). It's not essential to delete the XP entry; although it will be restored/replaced during XP repair routine even if you do delete it. Once W2K-Server starts its installation, the XP entries are redundant anyway - until XP repair is completed... and then they are overwritten or replaced as need-be.
When W2K Pro or Server go in (and similarly '9x) access to XP 'will' be lost - albeit temporarily. (The installation is still there - just not accessible, until an XP repair routine is completed.) This is because the older OS don't recognise a newer OS; and XP is the new boy/girl on the block - and is in effect invisible to the oldies... The XP mbr is overwritten/replaced by the earlier OS version (in this case W2K). The Repair routine restores the XP version of the mbr, its version of boot-files, and thus access to XP - setting it up as the controlling boot-loader.
You run W2K-Svr setup from either a CD boot (and the bios almost certainly will allow that judging by your laptop specs.), or use the 4 W2K boot-floppies/disks. If you don't have the floppies - you can make a set of W2K boot-floppies from the makeboot util (on the W2K CD) amd use those to boot/run setup.
Before you delete W2K-Pro visit the W2K-Pro 'help files' and look for the 'how to make to boot-floppies/disks' item (it's complete and very simple to follow). Or you can go to bootdisk.com, download a set of images and (self-)expand each to a floppy and use those.
Personally I'd make my own; it's useful exercise to be familiar with - in case of need...
Do not run Server setup from inside any installed OS (in this case XP - as you will have already deleted Pro).
Hope this clarifies it all for you?
Post back if need more input.
I'm going to be away/off-line from late morning tomorrow (GMT time-reference/zone) until next Thursday late pm., but I will check in here again later this evening and possible tomorrow am before leaving... in case..., although there are others here too who will help you out if need-be (I'm thinking of Wanderer in particular, or Michael #1 - if he's still around, and the Count...).