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If you check the options.ini files in the non-remote save directory and look at the steamcloud= setting that will tell you which directory the game is using (1=the 250900 remote folder, 0=the same folder as the options.ini) on a per computer user account (not per steam account, per computer account) basis.
Once you know which save files you need to copy over and where to it's just a simple copy&paste job (via USB or anything else suitable to transfer files from computer to computer of course). The files you want will be named something like persistentsavedata#.dat with #=1, 2, 3. In the non-remote folder with the options.ini files the game version is determined by folder and all have the same filenames. In the remote folder used by the cloud afterbirth files are prefixed by ab_ and afterbirth+ files are prefixed by abp_ so copy/paste which file you want to transfer - also rename as appropriate if the steamcloud= options are different for each of you (or just change yours to be the same as his to make things easier).
Note that if it's a shared computer with only 1 computer user account there will only 1 options.ini file, most likely with steamcloud=1 (if =0 then it'd be using a shared save file regardless of steam account anyway in this scenario), and you'll just have to copy the files across the 2 remote folders for the game (1 per steam accountID)