There is some stuff in the Building Regs that covers the position of flues (Part J if I remember correctly) but I don't think this is all you need to comply with. Take thescruffs advice to have your installer call.
http://www.planningportal.gov.uk/england/professionals/en/4000000000503.htmlGenerally: It can go straight out through a wall (eg It doesn't have to go through the roof) but there are restrictions on how close it can be to openings. It can be below the level of windows as long as it and they meets other restrictions.
Don't forget that the make and model of boiler may impose it's own restrictions.
Our boiler (a recently installed Grant) is floor mounted against an outside wall. The flue goes straight through the wall horizontally at a height of about 3 foot and terminates right there. It's all of about a foot long.