You can start with focusing the lenses on the base board. First you have to set the height adjustment at the bottom of the column to zero (and possibly screw the big adjustment screw all the way to the bottom too). Next you loosen the small locking screw on one of the lenses (the 100 on the picture) and very carefully focus a negative on the baseboard. Lock the screw and you're done. Repeat for the other lens. That should be enough for the autofocus for both lenses.
At the bottom of the column there should be a ring that could be set to different heights. (There are a couple (or three) set heights which corresponds to Leitz original easels.) Anyhow, unless your easel is of one of those heights, you can set it to zero and then adjust it with the big twist grip at the bottom until it's the correct height. (The second picture have the ring on the bottom and the big twist grip on top of the picture.)
As my favourite easel is of "non standard Leitz height", I've set the ring with the set heights at a height slightly lower than my easel and put a piece of metal to adjust it to the height I want. Then I don't have to worry about the twist grip unscrewing itself.
You can use any lens, but the AF only works with the lenses that you got. While I love my focomat IIc, I know that there are better lenses (which sounds strange as we are talking about a Leitz). The problem is that the lenses really needs to be exactly 60 and 100 mm for the AF to work. (E.g. the Schneider Componon-S 100 can be anything between 95 and 105 mm.) If you really like your enlarger and plan to use it a lot, plus have a lot of money, check out
Kiensle who sells a calibrated set of Componon-S lenses for your Focomat at a probably very hefty fee.
(One way of looking at it is to consider the fact that this enlarger cost about the same as a new Volvo Amazon in the -60'ies. So spending a "few" $$ on upgrading the lenses to be on par with the rest of the enlarger is money well spent.)
I normally stop the lens down by 2 stops. Most lenses have their sweet spot there.
Eh, yes... I nicked the pictures from an infamous auction site... Easier than processing and scanning pictures of my own focomat.
//Björn