What Fips does is make a new primary partition out of the free space in your hard disk. This is an inherently dangerous operation and it's a good idea to back up all your important data lest something go wrong. Having said that Fips has been used successfully by a large number of people in different conditions and unless there is something already wrong with your hard disk, FAT (File Allocation Table) or partition table things will work just fine. You should read the Fips documentation.
Before you set out to partition the hard disk you have to decide how you want to boot into Linux. The default and most common method is to use Lilo – a simple and basic bootloader program that overwrites (after saving) your hard disk's MBR (Master Boot Record) and on booting the system gives you a choice between booting either Windows or Linux. If you select Windows it boots Windows and you are met with the familiar windows screen or if you select Linux it boots Linux and if you don't make a choice in the stipulated time – could be anything from ±5 seconds depending on on how you set it up – it boots the default operating system, Windows or Linux, again depending on how you set it up. You can restore your original MBR anytime, when uninstalling Linux for instance, either by typing /sbin/lilo -u within Linux or typing fdisk /MBR in DOS (this will overwrite the MBR with the original Windows MBR) needless to say you would lose the option to boot into Linux after this and thus access to your Linux partition.
The problem with using Lilo especially for those with large disks is you would have to give up a substantial chunk of your disk space to Linux. This is not a flexible solution since while you can access your Windows partition from within Linux – the large MPEG files can thus be stored in Windows and accessed by both operating systems – the alternate is not true.
This is because of an arcane BIOS limitation that limits Lilo to the first 1024 cylinders of the hard disk. Windows and Linux have no such limitations – it has something to do with address translation and LBA which I have yet to fully understand. Suffice to know the BIOS cannot access data that is beyond this 1024 cylinder limit and since Lilo is dependent on the BIOS to boot the OS's nor can it. Thus if you want to use Lilo to boot Linux you got to make sure that the Linux partition is well below the 1024 cylinder limit. My hard disk – and most modern hard disks have more than 1024 cylinders – has 1650 cylinders and using Lilo means making the Linux partition at about the 1000 or 1010 cylinder mark which translates into a whopping 5.2 Gb of 12.9 Gb to Linux and this wasn't working for me since my Linux stuff hardly need more than 2 Gb and my Windows data on the other hand with MP3's and MPEG movies needs a lot more than 7 Gb.
The solution, and in Linux there are always solutions, is Loadlin, an underrated alternative to Lilo which is inexplicably not as popular or widespread, inexplicable because it's far more flexible. If you intend to use Loadlin and for those with large hard-disks it's an excellent alternative you don't have to worry about the 1024 cylinder limit. Even better you can launch Linux from your Windows desktop and modify your autoexec.bat file to give you an option to boot into either of the OS's during boot time not unlike Lilo. You are then free to size your partitions as you please. In my case a 2.2 Gb extended partition with 3 logical partitions. That's right 3 partitions. It's normal to make three partitions, one for the Kernel boot files, one for the root partition and one for the swap partition but more on that later.
If you must use Lilo but are unwilling to give up a lot of space there is a solution. Place the Linux partition in the middle of the disk. You have to split the new partition you just created using Fips into 2 (you would have to use Fips once again for this) the first partition which falls within the 1024 cylinder limit can be used for Linux and the second you can use for Windows. Thus your hard disk will then have 3 partitions the first and third for Windows and the one in the middle for Linux. I don't like this arrangement but it's up to you. (At the moment we are refering to the Linux partition as one but during the installation you will split it into 3 using the Linux tools) You can also make a small 15-20 Mb /boot partition and place it before the 1024 cylinder mark and the rest of the installation anywhere on the hard disk but again I quite don't like this.