The ally chosen is the first one available in your party (top to bottom in your party screen) by defaut

There are settings in the file \bin\Win64_Shipping_Client\config.json that you can change with any text editor, set them to true/false to enable/disable them. 
The settings are:
"onlyControlCompanions"                 - makes you only able to switch to companions                                                                                       - Disabled by default.
"controlRandomUnits"                       - makes the ally chosen random                                                                                                                 - Disabled by default.
"prioritizeCompanions"                      - makes you switch to companions first                                                                                                    - Disabled by default.
"allyControlledTakesCommand"       - makes you able to command your troops even after you switch                                                         - Enabled by default.
"onlyControlTroopsFromYourParty" - makes you only switch to units in your party, you won't switch to a unit from another lord's party - Disabled by default. 

The game will show the wrong weapons that the ally you are controlling is using, but it fixes itself after you switch weapons.

Make sure to create a backup save because others bugs that I don't know of could occur.

If you want to choose the unit that you control you should check LargerThanLife's mod: Post Mortem Possession