1. 利用默认的目录结构无需配置不同版本的工程目录结构
   只需在src\main的同级目录下新建渠道名称

2. 依赖的模块在构建时如果存在多版本，应该指明使用什么版本或者模块里头配置defaultPublishConfig属性

方案一：

dependencies {
    compile fileTree(dir: 'libs', include: ['*.jar'])
    compile 'com.android.support:appcompat-v7:21.0.0'
    flavorOneCompile project(path: ':testmoduleone', configuration: 'flavorOneDebug')
//    flavorOneCompile project(path: ':testmoduleone', configuration: 'flavorOneRelease')
    flavorTwoCompile project(path: ':testmoduleone', configuration: 'flavorTwoDebug')
}

方案二：

android {
    defaultPublishConfig "flavorOneDebug"
}

运行阶段在Build Variant窗口进行选择运行何种版本

灵活使用buildConfigField
如外网内网包可配置不同版本或者定义不同常量

android {
    ...
    buildTypes {
        def BOOLEAN = "boolean"
        def TRUE = "true"
        def FALSE = "false"
        def LOG_HTTP_REQUESTS = "LOG_HTTP_REQUESTS"
        def REPORT_CRASHES = "REPORT_CRASHES"
        def ENABLE_VIEW_SERVER = "ENABLE_VIEW_SERVER"
        def ENABLE_SHARING = "ENABLE_SHARING"
        def DEBUG_IMAGES = "DEBUG_IMAGES"

        debug {
            ...
            buildConfigField BOOLEAN, LOG_HTTP_REQUESTS, TRUE
            buildConfigField BOOLEAN, REPORT_CRASHES, FALSE
            buildConfigField BOOLEAN, ENABLE_VIEW_SERVER, TRUE
            buildConfigField BOOLEAN, ENABLE_SHARING, TRUE
            buildConfigField BOOLEAN, DEBUG_IMAGES, TRUE
        }

        client {
            ...
            buildConfigField BOOLEAN, LOG_HTTP_REQUESTS, TRUE
            buildConfigField BOOLEAN, REPORT_CRASHES, TRUE
            buildConfigField BOOLEAN, ENABLE_VIEW_SERVER, FALSE
            buildConfigField BOOLEAN, ENABLE_SHARING, FALSE
            buildConfigField BOOLEAN, DEBUG_IMAGES, FALSE
        }

        release {
            ...
            buildConfigField BOOLEAN, LOG_HTTP_REQUESTS, FALSE
            buildConfigField BOOLEAN, REPORT_CRASHES, TRUE
            buildConfigField BOOLEAN, ENABLE_VIEW_SERVER, FALSE
            buildConfigField BOOLEAN, ENABLE_SHARING, FALSE
            buildConfigField BOOLEAN, DEBUG_IMAGES, FALSE
        }
    }
}

Github:
https://github.com/eyyoung/GradleMultiFlavor