I have a 10GB hard drive that I am going to partition into, 2 partitions of approx. 5GB each.
On one partition I want Windows 2K on the other I want Windows 98 or possibly another OS, and I want to be able to specify what OS to load when I boot the system up?

My thoughts are
1: Will 1st create the partitions. 1st will be NTFS for Win2K, 2nd will be FAT32 for Win98SE
2: Install Win2K on NTFS partition
3: Install Win98SE on FAT32 partition

Does anyone have any advice for me? or Any experience with situations like this?

Yes. I have some advice for you. Install Windows 98 first. You can create the partitions ahead of time if you want but install 98 first, then install 2000. Windows 2000 will then ask which partition you want to install it on and you can format it at the time (during the installation) if you want. Or, just install it using FAT32 and you can convert from FAT32 to NTFS later on without any data loss. Windows 2000 will detect the Windows 98 OS and create the boot menu automatically for you so you can select which OS you want at boot up. It is a common thing that many people do and it is not complicated or unusual. Trust me on installing 98 first however. You can do it the other way but it is much more complicated and requires some configuration of the boot sector if 98 is installed after 2000. Good luck with it. It should work fine. Oh, did I mention that you want to install 98 first??

Post-1 (Glen) is one way to go, but I suggest a slight variation, which offers increased protection against crashes, etc...

It's the conventional/text-book approach.

Create a small FAT16/FAT32 C: (active Primary) system partition; create the Extended partition, and then sub-divide it into at least two (preferably three) logical-drives. Install '98 into the first 'drive'; W2K into the last 'drive. (As Glen advises it's better to install '98 first whenever you can in dual-boot '98/W2K...)

If you created at least three 'drives' then use the middle one for shared data (FAT32)...

This small C: system partition can be around 150-250Meg. Both OS's will install their boot/start-up files there; each OS will install its system files (the OS itself) into which ever 'drive' you point it to.

Each OS can thus be re-installed without affecting the other; each 'drive' can be reformatted without affecting the other; and if you have the third/middle (data) 'drive' then data is secure from either OS predations...

All you have to do is keep the C: system partition secure - do not lose the installed (boot) files, there otherwise no boot to...

Personally I would have C: as FAT16, even though both OS's can see FAT32 as well...

Your HD would thus resemble:

Primary:
c: = FAT16 (FAT32?) = 150-250Meg;
Extended:
d: = FAT32 = ???Meg. = '98;
e: = FAT32 = ???Meg. = W2K;

or
Extended:
d: = FAT32 = ???Meg. = '98;
e: = FAT32 = ???Meg. = data;
f: = FAT32 = ???Meg. = W2K;

I've done it a few times before and I just want to cast a vote for Glen. The idea from lm-s will work and it is, in fact, text-book...if you're reading a book about Linux. Oh yah, I don't know if you remember this part, but allow me to reiterate: Install 98 first. An OS is going to re-write the boot sector on install so you want the last one installed to be the one that can actually control dual-booting. So, install 98 first, make life easier.