A transistor exists where a polysilicon stick crosses either an N diffusion stick (NMOS transistor) or a P diffusion stick (PMOS transistor).
Note that there is no difference in the construction of a transistor source and a transistor drain. The source is determined as the source of conductors (electrons for NMOS / holes for PMOS) when current flows through the channel. In some pass transistor circuits, the source and drain may swap over during use.
Where two sticks of the same colour meet or cross there is always a connection.
Where two sticks of different colours meet or cross there is no implied connection.
Note that N and P diffusions may not cross each other. Where poly crosses diffusion we have a transistor (see above).
A connection may be explicitly defined using a filled black circle. In the general case a connection is permitted where the mask layers will be separated by just one layer of insulator (through which a "contact cut" may be defined). Thus P diffusion may connect to Metal1 but not directly to Metal2.
In a process where stacked contacts are permitted, we may draw a contact between non-adjacent conductors; e.g. between Poly and Metal3, in which case the connection to intermediate layers (Metal1 and Metal2) is implied.
The tap represents a connection to something we can't see; either the N-Well (not shown on our stick diagram) or the wafer substrate. A tap is defined using an unfilled black square. Here there will be only one conductor crossing the square (Metal1 power or ground rail).
An N-Well Tap is inferred where the connection is from a power rail while a Substrate Tap is inferred where the connection is from a ground rail.
We can often save space by using a combined contact and tap. Here the tap shares the same Active Area as the contact. A combined contact and tap is defined using a filled black square in place of the source contact (filled black circle).
A combined contact and tap can only be used where the end of a diffusion stick coincides with a contact to the power or ground rail.
If you deviate from these colours you will need to include a key with your stick diagram.