This is a very normal thing and no big deal. Just cite the other one with whatever the citation format is. Obviously you won't have a volume number or page numbers and add "In preparation." Or "Submitted." Or "In press." (Whatever applies.)
Note: that some reasonable portion of such prospective citations don't ever turn into articles or go into alternate journals or whatever. But such is life. No big deal. You are being as honest and accurate as you can at the time doing the citation. It is still possibly useful to a future researcher for years in the future, who may want to look for related papers when looking at the one paper. You are doing the best you can.
Note 2: There may be very good reasons to have separate papers like this. For example if you discovered and characterized a new important chemical with new apparatus, you may want to go into lots of detail on the chemical but not in detail on the apparatus for a chemicals journal...and then the converse for an apparatus journal. In addition, sometimes work has natural break points (chemical A and chemical B discovered with some connection) where it is really better for the reader to get an LPU (least publishable unit) on A and one on B. It's a judgment call and some people think it is done to pad count, but I actually prefer LPU papers because they are a bit more readable and focused. You can do a review paper later that combines some of them. Also LPUs are faster to get out.