You can go to your LBS as long as they’re in the scheme
Ask your LBS if they are, lots are nowadays.
or do a postcode search here http://www.cyclescheme.co.uk/
Then once you’ve found the bike you like, say for a grand, you go back to your work and fill out the form they give you, you may have to provide details of the LBS.
Then you wait a long time, about a month, for the voucher to arrive. IN the meantime your company has stepped into action and will have set up the pre tax removal of money from your pay packet, they should tell you how much it is and when it starts.
Once you have the voucher, march cheerfully to your LBS, present it and they’ll do the rest.
At the end your company will take 25% value of the bike off you, or the bike. But I expect that’s a negotiable thing for most companies.
edit: So to answer your question properly, yes. If you can sort out some extraordinary discount with your LBS, your company doesn’t care.