If in the first independent claim I say "an X comprising at least one guide mark on the first side" can I then say in a following dependent claim "the guide marks are also on the second side"? Does the "mark" becoming "marks" screw up the antecedent flow, or is it okay to jump to a plural spelling of the word.
Yes, 'marks' lack antecedent basis. You have positively declared one mark, with the possibility of more marks*. Your dependent claim must introduce additional marks if you want to switch to the plural.
How you go about it is up to you and the rest of the claim language. One possibility is 'at least a first guide mark' in the independent claim, with a dependent declaring 'at least a second guide mark on the second side' If you're declaring the location of all the guide marks, you can follow Eric Shain's comment, and say 'the one or more guide marks are on the second side'. But you may be limited in describing how one mark relates to another mark.
* As a side note, while many practitioners prefer the 'one or more' (or 'at least one') the courts have said that 'a'/'an' does not mean only single element (as long as the claim is open-ended (i.e. a the preamble says 'comprising'). So if you have 'a guide mark' and an competitor has two guide marks, they infringe on your claim. See Baldwin Graphic Systems, Inc. v. Siebert, Inc., No. 07-1262 (Fed. Cir. Jan. 15, 2008) described in more detail at https://www.lexology.com/library/detail.aspx?g=b7cca4cf-1482-4df3-9ba1-5d8e9770e923