The modulation Matrix is shown in the display as three columns and 8 rows. Each row is one modulation. The left entry in a row is the Modulation source. Here you select things like LFOs, envelopes, keytracking, modwheel, aftertouch pressure, etc.. The middle column is the intense of a set modulation, also named modulation amount. The right column is the destination which is modulated. You can use the pitch (that is the frequency of all 3 oscillators, individual oscillators and many, many parameters.
Some modulation sources are not routed straight to the modulation destination. but changed in the modulation amount by the Modwheel ("xMODW") or the Aftertouch pressure ("xPRS") or the VCA envelope ("xENVA").
There are some more exotic Modulation sources at the end of the modulation source list after Pressure. Many of these are unique to this Waldorf and are not recommended for beginners or not used in 99,99% of all factory patches. The same for the last 6 entries in the modulation destination list.
You find the modulation source and destination list in the appendix of the manual.
Examples:
1) Modwheel used to open the filter cutoff all the way
MODWHEEL +63 CUTOFF
2) LFO1 modulating the volume using the Modwheel to fade this modulation in
LFO1 xMODW -63 VOLUME
3) Changing the keytracking of oscillator 3 a bit flat
KEYTRACK -63 to +63 OSC 3 PITCH (experiment with the right modulation amount so it sound not to dissonant. Use only lower modulation amount values)
4) Introducing the drive distortion using the aftertouch of your keyboard. Set the DRIVE parameter to a low value before adding the modulation amount.
PRESSURE +63 (or less) DRIVE
5) Introducing NOISE in the mixer by using the Filter Envelope. Set the Noise level to a low value before applying the modulation.
ENVF +63 NOISE LEVEL
I hope this helps a bit.