Trying to sync apps in itunes after a complete computer reboot-

I recently cleaned out and rebooted my Macbook Pro from scratch and am now trying to organize my apps which exist on my iPhone 4S with my iTunes library. We have several Apple products using the same iTunes library, but we manually select which apps go on which device (i.e. my iPhone has a select number of apps that I like, and the family iPad mini has many others).
When I plugged my iPhone into the computer to see what iTunes would do it just showed me my iPhone screenshots on the rights, but not the offering of apps on the left. I was thinking of syncing the iPhone with iTunes then and there but a warning came up to say that it only syncs from computer to iPhone, and not the other way around. I didn't want to wipe out my apps on the phone so I didn't do it. Instead I went into my purchases on the iTunes library and downloaded them all again (I can see the files downloaded in users/Music/iTunes Media/Mobile applications as .ipa files). Not sure if this was the right move because while I could now see almost all of my apps in the iTunes apps window to sync to my iPhone, it seems to want to put ALL OF THEM on my phone at all times.
I've tried to "remove" the ones I don't want, but they seem to come back on my phone anyway. Not sure how to sync or not; I feel that I'm missing a specific command somewhere in iTunes to let me get rid of apps I do not want.
Right now I'm not backing up or syncing my phone with iTunes automatically (although I have played with it since the reboot), but I know I'm missing a step, or made a mistake when loading the apps back in.
Can anyone help out?
Thanks

Nevermind, it's restricted that's why it's greyed out.

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