OK, the way I do this is firstly make a file that has all the big components in it. In Siege (as an example), the big component was the castle and bridge and terrain - as those things are going to determine the placments of everything else. Thats your base file (File 1). Save it. Now comes making the next file. I reload File 1 and remove everything that isn't in the place that you want to put objects in (and group whats left). When I was putting people on the bridge in Siege, I deleted everything in File 1 but the bridge. Then I put all the objects in that I want tp put into that part of the scene (i.e. put the people on the bridge). At the end, I delete the bit of File 1 I used in this bit of the scene (i.e. delete the bridge), just leaving the newly added bits to the scene (the people on the bridge). Then save that (File 2). Keep doing this, making new files as you go for each batch of objects. At the end, merge all files together. Hope that helps.

Dreams are just nightmares on prozac...
Digital WasteLanD