Yes, you can use an indexer, but you a little over the recommended limit. You will have to review your server hardware and workload to see if it can support the extra work. If you find that after you configure the deployment server that it should be on it's own server, then the configuration can be relocated to a new server.
You can manage the inputs.conf and outputs.conf, but you will need at least two apps, one for windows and one for unix. If all of your windows and unix configs are not exactly the same, then you will need additional serverclasses for them.
The quick 'developer minded' guide for setting up and troubleshooting a deployment server can be found here:
http://wiki.splunk.com/Deploy:DeploymentServer
The Splunk documentation for configuring a deployment server can be found here:
http://docs.splunk.com/Documentation/Splunk/latest/Updating/Aboutdeploymentserver
Take the time to read and understand the material. A deployment server is very handy, but it must be configured correctly and each configuration is specific to the deployment - there is no magic plan that works for everyone.
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