If you let the master cylinder bleed to the point where the reservoir goes completely empty, you can introduce air into the bore cylinder. If this happens, you will need to bleed the master cylinder before bleeding the rest of the entire brake system, which adds a lot more work. Personally, I wouldn't recommend your idea. You should either pressure bleed them or vacuum bleed them. First, use a turkey baster or similar tool to suck most of the brake fluid out of the reservoir and then refill with clean fluid. Bleed the system as follows: right rear, left front, left rear, right front...occasionally stopping to check the fluid level in the reservoir and top off as necessary. If you have a second person to help, I would just pressure bleed it. If you don't, I've used a vacuum bleeder kit for years and it works great. Here's a similar kit to mine for $25 that should work:
http://www.ebay.com/itm/2-In-1-Brake-Bl ... 1265672658