You can recover your system or files while Windows is running from within Acronis.
Just choose the "Recover My Discs" option or "Recover My Files" option, whichever is appropriate for what you want to do.
If you are restoring a disc, (the OS for example) it will then show you all your Backups. Choose the one you want and hit proceed.
Acronis will prompt you to restart your computer at which point it will wipe the drive, and restore the image.
If for some reason you can not boot into Windows, you will need to boot from the rescue CD.
It will be the same procedure once Acronis boots, but you may need to point it to the location your backups are saved.
I strongly recommend burning a Recue Boot Disc just in case. You never know when it may be required.
Not only for a case in which Windows will not boot, but also if you replace your HD and want to restore the entire image to the new drive.
The option to do so is in the Tools menu, and it will guide you through the process.
For the most part, a restore can be initiated from within Windows, and complete upon reboot.