I hate to be the bearer of bad tidings, but this quote (from the BBC Watchdog website) isn't exactly reassuring!
"All of our volunteers struggled with their instructions and the tools often seemed inadequate for the job. All five made crucial mistakes that left their bikes unsafe to ride".
http://www.bbc.co.uk/.../flat_pack_bikes.html
My husband has recently put together three and had no trouble - they were only little bikes though (think one might have had gears). There was some swearing but that was because of the 'help' he was receiving, not the difficulty. They come with all the tools too.
Usually its a case of attaching the front wheel and reconnecting the front (V) brake after the wheel is in and turning the saddle and handlebars to the correct positions (will arrive positioned so they fit in the delivery box). The more difficult parts will be fine tuning the gears and brakes so they work correctly. The supplied spanner/tools are usually rubbish.