`Regardless, the clock pins will already be connected on the PCB, so you have to assign it manually anyway (regardless of whether its Xilinx or Altera).`
I did not understand this above sentence and I think you are experiencing problems understanding my problem. Maybe you have not done any design that challenged you with the pins. First you need to understand that putting a input clock to dedicated clock pin is not the end. Even though you do that the design may not work. See below for the error
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Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in target device due to device constraints
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_1 because location is already occupied by node "deserializer:tile1_deserializer|altlvds_rx:ALTLVDS_RX_component|deserializer_lvds_rx:auto_generated|lvds_rx_pll"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_2 because location is already occupied by node "deserializer:tile6_deserializer|altlvds_rx:ALTLVDS_RX_component|deserializer_lvds_rx:auto_generated|lvds_rx_pll"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_3 because location is already occupied by node "deserializer:tile5_deserializer|altlvds_rx:ALTLVDS_RX_component|deserializer_lvds_rx:auto_generated|lvds_rx_pll"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_4 because location is already occupied by node "deserializer:tile4_deserializer|altlvds_rx:ALTLVDS_RX_component|deserializer_lvds_rx:auto_generated|lvds_rx_pll"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_5 because location is already occupied by node "deserializer:tile2_deserializer|altlvds_rx:ALTLVDS_RX_component|deserializer_lvds_rx:auto_generated|lvds_rx_pll"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_6 due to device constraints
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_6, because the PLL I/O pin Pin_T10 with port type INCLK is already occupied by node "iTile1SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_6, because the PLL I/O pin Pin_T9 with port type INCLK is already occupied by node "iTile2SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_6, because the PLL I/O pin Pin_L10 with port type INCLK is already occupied by node "iTile3SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_6, because the PLL I/O pin Pin_L9 with port type INCLK is already occupied by node "iTile6SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_7 due to device constraints
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_7, because the PLL I/O pin Pin_T10 with port type INCLK is already occupied by node "iTile1SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_7, because the PLL I/O pin Pin_T9 with port type INCLK is already occupied by node "iTile2SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_7, because the PLL I/O pin Pin_L10 with port type INCLK is already occupied by node "iTile3SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_7, because the PLL I/O pin Pin_L9 with port type INCLK is already occupied by node "iTile6SerClk"
Error: Can't place MPLL or GPLL PLL "mainpll:mainpll_inst|altpll:altpll_component|mainpll_altpll:auto_generated|pll1" in PLL location PLL_8 because location is already occupied by node "deserializer:tile3_deserializer|altlvds_rx:ALTLVDS_RX_component|deserializer_lvds_rx:auto_generated|lvds_rx_pll"
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TO SUM UP
I will have 8 incoming clocks
I do not know by heart which one should go to bank 1 which one should go to bank2
If I do myself tool gives errors.
I will make the tool auto-assign pins. (see it is not manual)
I want to use this information