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What about mail and wifi settings? Will they be lost?

Wifi settings aren't synced, so no, syncing shouldn't affect them. Mail can be synced or not, there's a place in the device's iTunes tab to set this up. If Mail is not set to sync, then again, syncing shouldn't affect it.
 
Managing to devices on same conmputer?

I have a couple of iPad and a few other iOS devices ont he same computer.

How can I keep an app I put on my iPhone from showing up on the iPad, or vice versa?

It seems like when I sync, I get back apps that I had deleted.

Thanks!
 
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