Let me start by saying you should not consider doing an in-place upgrade of StoreFront 1.2 to 2.0. I suggest you start with a new deployment.
Although I was able to get the upgrade working as a personal challenge, I don’t think it is a clean way to go about it. You can read more about some known issues on this Citrix StoreFront 2.0 upgrade and install issues article
Now after you have your StoreFront 2.0 “Web Interface” servers installed… lets make some changes. Note that the changes below will be replicated to other StoreFront servers in your Server Group, so you don’t have to make changes on multiple hosts 
Environment:
- Windows 2008 R2
- Citrix XenApp 6.5 Hotfix Rollup Pack 2
- PVS 6.1.16
- StoreFront 2.0
Remove “Activate”
If you are not using provisioning file to configure your Receiver, open the web.config in the C:\inetpub\wwwroot\[Store]Web\ directory
Locate the following:
<receiverConfiguration enabled=”false” downloadURL=”ServiceRecord/GetDocument/receiverconfig.cr” />
Change the value from “true” to “false”
Disable Desktop auto-launch
By default, a single XenDesktop or Full Desktop XenApp will auto-launch for the user
<userInterface frameOptions=”deny” autoLaunchDesktop=”false“>
Change the value from “true” to “false”
Show Apps as default instead of XenDesktops/Full Desktop XenApp
<uiViews showDesktopsView=”true” showAppsView=”true” defaultView=”apps” />
Change the value from “desktops” to “apps”
Change Logos
Receiver for Web provides a built-in support for customization through the contrib folder. This folder is located under the Receiver for Web site in the file system (default location is C:\inetpub\wwwroot\sites\Citrix\StoreWeb\contrib) and contains the built-in customization hooks. It is recommended that all customization code and media are stored under this folder because the content of this folder will be preserved upon upgrade to the subsequent releases.
Using the contrib folder you can upload your logos and create syntax such as below. You will need to change height, width and margin based on your logos
#credentialupdate-logonimage, #logonbox-logoimage {
background-image: url(“company_whiteTrans.png”);
height: 64px;
width: 353px;
}
#header-logo {
background-image: url(“company_whitetrans_small.png”);
height: 31px;
margin: 8px 0 0 22px;
width: 179px;
}
Set StoreFront as the Default Page within IIS
Now… Lets set that StoreFront site as you default site, as we recall with the legacy Web Interface component, each Web site had the option to be the default page for the IIS site. This option is not available in Storefront. 
To make a Storefront Web site the default page within the IIS site, complete the following procedure:
- Open Notepad and paste the following text:
<script type=”text/javascript”>
<!–
window.location=”/Citrix/StoreWeb”;
// –>
</script>
Note: Replace /Citrix/StoreWeb to the correct path to your Store’s Web site, if required.
- Select File > Save As and browse to the IIS folder, by default the C:\inetput\wwwroot is the IIS folder.
- Select the Save as type to All types.
- Open IIS Manager.
- Select the SERVERNAME node (top-level) and double-click Default Document, as shown in the following screen shot:
- Select Add…, and enter the file name of the .html file provided in Step 4.
- Ensure the .html file is located at the top of the list, as shown in the following screen shot:
- Open the command prompt and run the following command:
IISRESET
You can read more info on this under this CTX article
