"I guess I can still place my sensors at these pins, even though they are marked other functionality? "
Yes you can, but of course can't use multiple functions at the same time for the same pin.
"However, when using TX1 and RX1, does that mean I loose one of the serial communication lines? "
Yes, can't use Serial1, but that still leaves three other hardware serial ports using pins 0 & 1, 14 & 15, and 16 & 17. And of course there is a software serial library routine available that allows one to utilize serial communications on any free pair of digital pins.