1) You manage it like any other VM, each Linked Clone if deployed properly will be unique as if you created X number of VMs. What I mean by this, assuming you're cusotmizing each guest whether that's Linux/Windows such as providing/setting a unique IP/hostname for each guest or even joining your Widnows system to AD. In terms of the vCenter management, all things that vCenter provides still hold true such as DRS/HA ... some things that may not work are sVMotion since your Linked Clone has its own delta disk but also references the parent base disk and you want to keep all those within a datastore. Havind said this, I know that you can have your base sit on one datastor and create your linked clones on another datastore and they'll function perfectly fine. It all depends on the requirements and how you create/deploy your Linked Clones.
How you manage your individual Linked Clones and the base in terms of updating/re-deployment gets a little complicated because there's few ways of doing it and that is probably driven by your use case and what you need.
2) Yes, as of vSphere, there's been some new APIs introduced that allow you to officially create Linked Clones and you are not required to use View or Lab Manager to created Linked Clones. View does provide some added benefit for some higher level abstraction and some nice management features via the the GUI, but again majority of the features can be re-created using the vSphere APIs.
Here are some additional links that may be helpful including a vShpere SDK for Perl script that shows you how you can implement Linked Cloning, also VMware white paper on how to use the new API functions and some shell scripts that implements Linked Clones in ESX(i) 3.x.
Linked Clones on vSphere: http://planetvm.net/blog/?p=777
Here's another great read on how Linked Clones work in View and they can function simliar if you use the APIs to create, just depends on how you design the setup.
http://rodos.haywood.org/2008/12/storage-analysis-of-vmware-view.html
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William Lam
VMware vExpert 2009
VMware ESX/ESXi scripts and resources at:
Twitter: @lamw
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