Is it best to create a separate partition to install ubuntu on, if so how big should it be. I install it onto my big hard drive but when I am in ubuntu I cannot access any of the files on that drive as they are all in root.
It is part of Linux security that you can not access files owned by root as a normal user. It has nothing to do with partitions as such.
You should however have a separate ext4 partition for your Ubuntu installation if you are doing a full installation. If you install within Windows this is called a wubi install.
A wubi install is OK if you want to try Ubuntu, or if Windows is still your primary operating system. To do a full Ubuntu install you would need to make a bootable Ubuntu disk or USB (LiveDVD or LiveUSB) and boot off that to start the install.
For a minimal install of Ubuntu you would need about 8GB (recommended) for the operating system, plus enough space for whatever data you intend to have in your /home directory. In actual fact Ubuntu will install in under 4GB but this does not really allow for any room for maintenance updates or installing other programmes.
To access files owned by root to change things in Linux it's necessary to prefix commands with 'sudo'. For example to update the system from comand line the command is "apt-get update" however as a normal user you will get a permissions error if you do this. The correct command for your admin user is:
which will update the files list, and
to actually download and install any available updates.
The main area where your user has normal access to is /home/username. Some of the configuration files are kept there so that each user can have their own working environment, and all of the data is also kept there.
Advanced partitioning topic:
You can have a separate partition for /home if you wish, and this keeps data separate from the / partition. When Linux boots this separate partition is mounted at /home so that it works seamlessly, as it now appears to be part the / filesystem. There are some advantages to this, such as making it easier to re-install or upgrade, and the extra safety of having system files and data on separate partitions or even different drives.