Again, I am not familiar with the FreeScan software, but with all of the frequencies for Marin entered as trunking site frequencies the scanner should lock onto the active control channel and then you should receive transmissions on the talkgroups you have entered. Although I am not familiar with the Marin System, I have been monitoring many similar systems over many years using the 396xt and the 325P2 which program the same way and use the same Butel software. (If you have a few more dollars to spend I would suggest purchasing the Butel ARCXT or ARCXT PRO solftware)
RR indicates Sites 3, 4, and 5 are IntelliRepeaters. This means they fill in dead zones and only repeat transmissions when a radio is affiliated with one of them. I would take those frequencies out of the program to avoid your scanner locking onto one of sites rather than the East or West Zone.
I would suggest programing 2 separate sites, one East Zone and one West Zone. If you happen to be in an area or travelling where both zones are received it is easy to lock out the weaker of the 2 zones. If you have control channels from both sites active the scanner may jump between the two zones. I usually assign a quick key to each site but you could use one quick key and the lockout feature instead.
Also, the fact that Marin has an "East Zone" simulcast and "West Zone" simulcast suggests the possibility that some talkgroups may only be carried on one of the two zones. Years ago Eagle County Colorado had a similar system with East and West Zones, and the West Zone carried only talkgroups used in the Western half of the county. However, if a unit leaves the east zone and affiliates with the west zone the west zone site will carry the talkgroup as long as that eastern unit is in that area.It may take some time to figure out whether the 2 zones are indeed split.
The more you use the scanner the more you will learn. Direct importing from Radio Reference makes programming trunked systems very easy. ARCXT software lets you select what sites and talk groups to download, select quickeys and other options and in a couple of minutes you are all set. Comes in really handy for travelling. Also reduces the chance of making an error entering one of the many frequencies common in large systems.
Oh, in terms the simulcast problems mentioned earlier, I have found that with Motorola P25 type 2 systems the 325p2 does ok in most cases. Where it often fails miserably is with Motorola P25 PHASE 2 simulcast systems.
Good luck!