I'm assuming that you mean 'SIP Trunk account' - rather than SIP Trunk channel?
Usually a SIP Trunk account can be configured to support multiple channels, so if you need more call capacity, you ask your SIP Trunk provider to allow more simultaneous call capacity in the group [open up more channels].
If you have added a second SIP Trunk group, then you need to create outbound rules for extensions to use the trunk group. You might do this by assigning one trunk group to one set of extensions (i.e. Company A), and the other to the remainder of the extensions (Company B), or if you are using them as a pool for everybody, then you might just have one trunk group as the primary route, and the second as an alternative if the first is in use.
You have hit us with a fairly broad question, so have a look at this to see if it helps:
http://www.3cx.com/docs/manual/outbound-rules/
In regard to incoming calls, you need to assign the two trunk groups to two different incoming call groups i.e. each company has its own call group - or at least to two different extensions (one in each company). Note however, that call groups are not supported if you don't license the 3CX v.11 system.