Answering or Ending Calls
For the most part, you can both answer and end a call with one gesture: the two-finger double tap, also known as the "magic tap". Tap two fingers on the screen, then tap them again quickly. When you are receiving a call, this gesture will answer; when you are in a call, this gesture will end it. When ending a call, though, please note that you must remove the phone from your ear. This tells the phone to exit the mode where the touch screen is basically turned off, to prevent your face from activating commands as you talk. In essence, holding your phone to your ear deactivates the touch screen, so you have to let the screen re-activate before you can issue commands.
Sometimes, for reasons unknown, this gesture will not work. In that case, simply find the "answer call" or "Accept" button that will appear on the screen near the home button. Alternatively, bring up the phone app (which will launch when a call is answered anyway) and manage the call from there.
If you want to silence the ringer so you can better hear VoiceOver, press either volume button while the device is ringing. This disables the ringer without declining or answering the call, giving you the chance to hear VoiceOver and use the options available when a call is incoming.
Using Touch Tone Menus
Often, you'll have to deal with a menu during a phone call--selecting a department, entering a code, and so on. This is certainly doable on iOS, but it may take some getting used to if you're coming from a phone with a tactile keypad.
The first thing to remember is that, as described above, the iPhone will disable the touch screen when you hold it to your ear. To enter numbers on the keypad, then, you must lower the phone and wait for the touch screen to come back on. Unless you set it in Settings > General > Accessibility > Call Routing, this will cause your call to switch to speakerphone mode. It has to, or you couldn't hear VoiceOver telling you what key you're pressing, but this is important to keep in mind. For this reason--and because it can be easier to hear speech over the phone call audio--many people prefer to use a headset for this kind of call. You certainly don't have to, of course, but do remember that speakerphone mode will engage once the touch screen comes on.
The second thing to note is that you will need speech on to hear what keys you are feeling. Selecting a key is exactly the same as selecting a letter on the iOS keyboard; that is, it follows the typing mode setting you normally use. To enter a number during a call, just find the key and lift your finger (for Touch Typing) or double/split tap (for Standard Typing).
Should you find yourself with no keypad, just go to the Phone app and one should appear. There is also a Status Bar item when a call is in progress to quickly return you to your call screen. As of right now, you cannot use a bluetooth keyboard or braille display to enter numbers and have them picked up by the other party on the line.
Muting, Joining, and Other Call Management
While in the usual view you get when you make a phone call, you have a numeric keypad taking up much of the screen. Above it is the number (or name, if it's in your contacts) you've called and the time the call has lasted. Below it are buttons to end the call and hide the keypad. The latter button is how you bring up all the other calling options available. Double tap it while a call is in progress, and you should see your keypad replaced by several buttons--mute, add call, and more. All of these are very self explanatory; the thing I wanted to show you is how to reveal them. Should you need it again, there is a "Show Keypad" button in the bottom right of the screen which will bring your numeric keypad back.
Using iOS During a Call
You can use your phone like normal while a call is in progress, though VoiceOver's speech will be degraded to the same quality as the phone call's audio and may thus be difficult to understand. As of this writing, iOS is set up to mute your microphone whenever VoiceOver speaks, so no one will hear speech if you need to look at something during a call. Keep in mind that you can't talk over VoiceOver, since muting the microphone applies to your voice as well as your phone's. Remember, too, that using braille input can cause your phone to switch out of speakerphone mode if your hand covers the sensors near the top of the device. Finally, note that Siri and text dictation are not available during a phone call.