Hi there,
There are generally two types of connections used for subs: speaker-level and line-level. It sounds like you have been using speaker-level, but your new receiver also offers a line-level sub output.
If you want to continue using it they way you have been, you will need to connect your existing sub cabling to a speaker output on your receiver. If your new receiver has only one pair of L/R front speaker-level outputs, I think you should be able to get away with connecting the sub and main speakers in parallel (the sub input should have a high impedance, low current input, so it shouldn't change the behavior of the mains).
Now, it would be better to send that single RCA signal to your sub using a regular patch cord. Does your sub have an RCA input? Most do, unless perhaps they are from an HTIB or really old or Bose. It would be preferred to connect this way so that your receiver can apply its bass management to the sub signal.
If you can, let us know the makes and models of your receiver and sub, and perhaps we can find more information online.
Good luck!