Как то так:
QT += core gui
TARGET = howto
TEMPLATE = app
SOURCES += main.cpp\
mainwindow.cpp
HEADERS += mainwindow.h
FORMS += mainwindow.ui
SUBDIRS += qprocess
TEMPLATE = subdirs
SUBDIRS += Modules/Project1 \
Modules/Project2 \
Modules/Project3
CONFIG += ordered
TARGET = prjName
TEMPLATE = app
CONFIG += debug_and_release
CONFIG += warn_on
QT += ......
...........
TEMPLATE = subdirs
SUBDIRS += Modules/Project1 \
Modules/Project2 \
Modules/Project3
CONFIG += ordered
и имеем такие субпроекты: