If it's a wood stock made on a duplicator, they don't come out quite perfect. So you'll have to decide what's most visually appealing to you. If it's a flat top, and it's mostly flat you can average that, or you can level up the surface where the fore-end is and go off of that. Either way, you'll likely find you're going to end up truing it all up all the surfaces with the mill. Once you have it in place I've found its best to always make sure you level and square everything you can with it in the position it's in. That way you can flip it over and have a flat reference. Some of the decision you make will be determined by where you have the most "excess" wood that you can mill down and make true to everything else.
Once you've put it in, trued up everything you can, you can put the action screw holes in. And then cut out for the action and barrel channel. Once you've finished inletting, you can flip it over, and since the top will be flat, you will have your reference, and you'll just need to tram in the action screw holes you drilled for your left and right. Now you can make the fore-arm perfectly parallel with your action and each other. Its also a good time to true up the bottom of the forearm, and if you're doing a tooley style you can flatten out the tail and make everything true.
I realized this is getting long. A lot of it just comes down to personal preference, and experiences learned from mistakes made, or "better ways" found by doing so. If you have someone nearby who has done it, that can help. Or if you'd like I can talk you through some of how I like to do it. As sometimes its a little easier than typing it all out. If you'd like, pm me your phone number.
Hope some of that helps.