hey deep,
first of all i saw the attachment you have provided.. the settings seem to be right acc. to me. Actually these options depends on how you want your MTO data to be for a project, so generally these settings are defined acc to the project requirements..
For me i do not make frequent changes to these settings once they are been defined, so as to maintain uniformity amongst all the projects...
Coming to your points on how to make these settings..
Bolt length roundoff option -> sets the bolt length roundoff calc. As per 'your' settings the
bolt length will be calculated exact. Otherwise you can choose
other options like bolt length table in which you can define the
preffered bolt length (define in PJS) or give a roundoff factor
which will calc your length accordingly..
Length calculation -> sets which stud table to be used
i.e for Almost Precise - STUD_150_5
for Precise - STUD_20_150_5
Bolt commodity table -> sets whether commodity code for bolts are taken from PJS
(ie your pcd) or bolt commodity code table
Bolt diameter units -> sets the units for bolts diameter (english or metric)
Bolts length units -> sets units for bolt length (english or metric)
gasket search -> sets default or alternate gasket search default will take gaskets
defined in your pcd alternate will allow you to define gask. of diff
prp & the selection will be done by reference data.
General practice is to give 'default' option & provide optional
gaskets!!
COMMODITY CODE --
size independent -> commodity code is used from pdtable_202 i.e as defined in
your pcd material descp is used from the material descp. library
size dependent -> commodity code from pdtable_202 (i.e pcd) is used to retrieve
data from pdtable_211 or pdtable_212 as per the various
settings. Now this size dependent commodity codes will be
shown in the reports.
These various settings you will have to read from
the available PDS documentaion as its difficult to explain in one
go !! 
But in general we use the size independent toggle only..
Benefits for using ,for example pdtable_212 (implied material data), is that you can report the implied items for your main commodities in your reports as well as your isometric.
Eg:- In some cases flanges include an implied item like a flange cover (to prevent damage to the face finish).
So in the pcd we define a '+' sign in front of the commodity code to reflect that an implied item is used. Then the data for the implied item is stored in pdtable_212...
Again do refer the PDS help for more details.. or for instant help on a particular topic use the "help" button on your PDS form... it'll be gr8 help..
ciao
Abhishek