Having said that, for stack, you can adjust head tube length and/or top tube slope depending on what you're trying to achieve; these will change stack.
Re reach, I tend to figure out what the front centre needs to be, then work back from there to get a suitable top tube length/stem length/head angle/offset/trail, and saddle position/seat angle at the other end.
In rattlecad it's not always obvious which parameters are the driving ones and which are driven, and like most software rattlecad isn't well documented(!). Time and experimentation are your friends.
IMHO, it's best to start off from a "known good" fit, then use the contact points from that to fix the BB, saddle and bar centre in place; everything else can be adjusted to suit.
Stack and reach are useful for comparing frames but (IMHO) shouldn't be set in stone and used as primary inputs. YMMV.
Later,
Stephen
To change stack and reach you adjust the parameters that decide stack and reach - head tube length, top tube length, top tube offset on head tube, headset height, stem length and angle, and to some extent fork geometry. With RattleCAD you start with the contact points, not the other way around. http://rattlecad.sourceforge.net/howto.html